Diagnostics and therapeutics for diseases associated with kallikrein 9 (klk9)

ABSTRACT

The invention provides a human KLK9 which is associated with the hematological diseases, cardiovascular diseases, neurological diseases, metabolic diseases, urological diseases, cancer disorders, inflammation disorders, dermatological diseases and gastroenterological diseases. The invention also provides assays for the identification of compounds useful in the treatment or prevention of hematological diseases, cardiovascular diseases, neurological diseases, metabolic diseases, urological diseases, cancer disorders, inflammation disorders, dermatological diseases and gastroenterological diseases. The invention also features compounds which bind to and/or activate or inhibit the activity of KLK9 as well as pharmaceutical compositions comprising such compounds.

TECHNICAL FIELD OF THE INVENTION

The present invention is in the field of molecular biology, moreparticularly, the present invention relates to nucleic acid sequencesand amino acid sequences of a human KLK9 and its regulation for thetreatment of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in mammals.

BACKGROUND OF THE INVENTION

Proteases play a role in carefully controlled processes, such as bloodcoagulation, fibrinolysis, complement activation, fertilization, andhormone production. These enzymes are also used in a variety ofdiagnostic, therapeutic, and industrial contexts. KLK9 is a member ofthe group of protease enzymes [Mason et al. (1983), Yousef and Diamandis(2000), Yousef et al. (2001), WO0179466, WO0200860, U.S. Pat. No.6,287,561].

Proteases were recognized very early in the history of biochemistry. Inthe nineteenth century, one primary focus of research was on digestiveproteases, like pepsin and trypsin. Proteases belong systematically tothe C—N Hydrolases. More specifically, proteases catalyze the hyprolyticcleavage of a peptide bond and are therefore called peptidases as well.

Proteases can be classified according to several criteria, e.g. bylocalisation. Digestive proteases are located in the gastro-intestinaltract. These proteases are responsible for the digestion of foodproteins.

Peptidases located extracellularly in the blood or other extracellularcompartments of the body play often regulatory roles in processes likefor example blood clotting, fibrinolysis, or activation of complementconstituents.

Intracellularly located proteases exhibit a wide variety of roles. Theyare found in compartiments like the ER, the Golgi apparatus, or thelysomes. Their functions include for example activation of peptidehormons, ubiquitin mediated proteolysis, among others.

Proteases are most commonly classified according to their mechanism ofaction, or to specific active groups that are present in the activecenter. The following groups can be distinguished:

-   1. Serin-peptidases, 2. cystein-peptidases, 3. aspartyl- or    acidic-peptidases, 4. metauo-peptidases, or 5. peptidases with yet    unclear reaction mechanism.    Serine Peptidases

Serine proteases exhibit a serine in the catalytic site which forms acovalent ester intermediate during the catalytic reaction pathway by anucleophilic attack on the carboxy carbon of the peptide bond. In theactive site of serine proteases a catalytic triad comprised of anaspartate, a histidine and the above mentioned serine is found. Thistriad functions in the reaction mechanism as a charge relay system.

To the large family of serine protease belong, for example, thedigestive enzymes trypsin and chymotrypsin, components of the complementcascade, enzymes involved in the blood clotting cascade, as well asenzymes that function in degradation, rebuilding and maintenace ofconstituents of the extracellular matrix.

One feature of the serine protease family is the broad range ofsubstrate specificity. Members of the trypase subgroup cleave afterarginine or lysine, chymases after phenylalanine or leucine, aspasesafter aspartate, metases after methionine and serases after serine.

Cysteine Proteases

During the catalytic reaction of cysteine proteases a covalent thioesterintermediate is formed by a nucleophilic attack of the cysteine on thecaboxy carbon of the peptide bond. Similar to the serine peptidases acatalytic triad comprised of the cysteine, a histidine and an asparagineis found which functions as a charge relay system to facilitate theformation of the thioester intermediate.

Members of the Cysteine protease family have roles in many differentcellular processes, e.g. processing of precursers or intracellulardegradation. Examples for cysteine proteases include lysosomalcathepsines, and cytosolic calpains.

Aspartyl- or Acidic Peptidase

The catalytic site of aspartyl proteases is composed of two aspartateresidues. At the pH optimum of aspartyl proteases (2-3) one of theaspartyl carboxy groups is ionized and the other is neutral, which isimportant for the catalytic reaction to occur. Examples for aspartylproteases are gastric pepsins A and C, chymosin, as well as mammalianrenin.

Metallo-peptidases

Metallo-peptidases are proteases, whose proteolytic activity depends onthe presence of divalent cations in the active center. Examples ofmembers of this class are carboxypeptidase A, which represents apancreatic digestive enzyme, the Angiotension Converting Enzymes (ACE),which are responsible for the conversion of angiotensin I to angiotensinII, or the Extracellular Matrix Metalloprotienases.

In summary, a huge number of proteases play a central role in severalimportant cellular and intracellular processes. Furthermore, the valueas pharmaceutical targets has been proven for several proteases. Forexample, the protease encoded by the HIV genome is used as a target fordrugs for the treatment of HIV infections, the proteasom complex hasbeen discovered as an anti-cancer target, or Cys-proteases have beenimplemented as drug targets for inflammatory disorders. Selectiveinhibitors have been developed as therapeutic agents for diseases suchas HIV. Thus, the identification of further disease implications ofprotease species and their splice variants may lead to the developmentof specific inhibitors or modulators, or suggest new utilities for knowncompounds affecting proteases. That in turn will provide additionalpharmacological approaches to treat diseases and conditions in whichprotease activities are involved. This diseases may include, but are notlimited to, infections such as bacterial, fungal, protozoan, and viralinfections, particularly those caused by HIV viruses, cancers, allergiesincluding asthma, cardiovascular diseases including acute heart failure,hypotension, hypertension, angina pectoris, myocardial infarction,hematological diseases, genito-urinary diseases including urinaryincontinence and benign prostate hyperplasia, osteoporosis, peripheraland central nervous system disorders including pain, Alzheimer's diseaseand Parkinson's disease, respiratory diseases, metabolic diseases,inflammatory diseases, gastro-enterological diseases, diseases of theendocrine system, dermatological diseases, diseases of muscles or thesceleton, immunological diseases, developmental diseases or diseases ofthe reproductive system.

TaqMan-Technology/expression Profiling

TaqMan is a recently developed technique, in which the release of afluorescent reporter dye from a hybridisation probe in real-time duringa polymerase chain reaction (PCR) is proportional to the accumulation ofthe PCR product. Quantification is based on the early, linear part ofthe reaction, and by determining the threshold cycle (CT), at whichfluorescence above background is first detected. Gene expressiontechnologies may be useful in several areas of drug discovery anddevelopment, such as target identification, lead optimization, andidentification of mechanisms of action. The TaqMan technology can beused to compare differences between expression profiles of normal tissueand diseased tissue. Expression profiling has been used in identifyinggenes, which are up- or downregulated in a variety of diseases. Aninteresting application of expression profiling is temporal monitoringof changes in gene expression during disease progression and drugtreatment or in patients versus healthy individuals. The premise in thisapproach is that changes in pattern of gene expression in response tophysiological or environmental stimuli (e.g., drugs) may serve asindirect clues about disease-causing genes or drug targets. Moreover,the effects of drugs with established efficacy on global gene expressionpatterns may provide a guidepost, or a genetic signature, against whicha new drug candidate can be compared.

KLK9

Kallikreins, a subgroup of serine proteases with a molecular weight of25,000-40,000, have diverse physiologic functions in many tissues. Theyhave the ability to release vasoactive peptides from kininogen in vitro,although the kininogenase activity of different kallikreins is highlyvariable. The true physiologic role of specific kallikreins is oftenunrelated to the kininogenase activity. In the mouse a major site ofkallikrein synthesis is the male submaxillary gland. Glandularkallikreins are also synthesized in the pancreas and kidney. The severalkallikreins found in this tissue include epidermal growth factor bindingprotein (EGF-BP) and the gamma subunit of nerve growth factor (NGFG)which are responsible for the processing of EGF and NGF, respectively.Although EGF-BP and NGFG exhibit strict substrate specificity, theyshare extensive amino acid sequence homology and immunologiccrossreactivity. Mason et al. (1983) concluded that the glandularkallikrein gene family comprises 25-30 highly homologous genes thatencode specific proteases involved in the processing of biologicallyactive peptides.

All kallikrein genes are closely linked on mouse chromosome 7(assignment by Chinese hamster-mouse hybrid cell studies). Several humankallikrein genes have been isolated. Based on homology between the humanand mouse kallikrein loci, Yousef and Diamandis (2000) defined a 300-kbhuman kallikrein gene region on chromosome 19ql3.3-ql3.4. Within thisregion, they identified a new kallikrein gene, KLK9, which theydesignated KLK3 (kallikrein-like 3), that contains 5 coding exons. Thededuced 250-amino acid KLK9 protein has a predicted molecular mass of27.5 kD and shares 40% amino acid sequence identity with KLK1(kallikrein 11).

RT-PCR analysis showed that KLK9 is primarily expressed in thymus,testis, spinal cord, cerebellum, trachea, mammary gland, prostate,brain, salivary gland, ovary, and skin. Lower levels of expression wereseen in fetal brain, stomach, lung, thyroid, placenta, liver, smallintestine, and bone marrow. No expression was seen in uterus, heart,fetal liver, adrenal gland, colon, spleen, skeletal muscle, pancreas, orkidney.

Yousef and Diamandis (2000) determined that the KLK9 gene is regulatedby steroid hormones in a human breast cancer cell line.

Many members of the human kallikrein gene family are differentiallyexpressed in various malignancies, and some are useful cancerdiagnostic/prognostic markers. Yousef et al. (2001) performed aquantitative analysis of KLK9 expression in ovarian cancer. The resultsindicated that KLK9 is under steroid hormone regulation in ovarian andbreast cancer cell lines. Immunohistochemically, the protein waslocalized in the cytoplasm, but not in the nuclei, of the epithelialcells of ovarian cancer tissues.

SUMMARY OF THE INVENTION

The invention relates to novel disease associations of KLK9 polypeptidesand polynucleotides. The invention also relates to novel methods ofscreening for therapeutic agents for the treatment of hematologicaldiseases, cardiovascular diseases, neurological diseases, metabolicdiseases, urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammal.The invention also relates to pharmaceutical compositions for thetreatment of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising a KLK9 polypeptide,a KLK9 polynucleotide, or regulators of KLK9 or modulators of KLK9activity. The invention further comprises methods of diagnosinghematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the nucleotide sequence of a KLK9 protease polynucleotide(SEQ ID NO:1).

FIG. 2 shows the ammino acid sequence of a KLK9 protease polypeptide(SEQ ID NO:2).

FIG. 3 shows the nucleotide sequence of a primer useful for theinvention (SEQ ID NO:3).

FIG. 4 shows the nucleotide sequence of a primer useful for theinvention (SEQ ID NO:4).

FIG. 5 shows a nucleotide sequence useful as a probe to detect proteinsof the invention (SEQ ID NO:5).

DETAILED DESCRIPTION OF THE INVENTION

Definition of Terms

An “oligonucleotide” is a stretch of nucleotide residues which has asufficient number of bases to be used as an oligomer, amplimer or probein a polymerase chain reaction (PCR). Oligonucleotides are prepared fromgenomic or cDNA sequence and are used to amplify, reveal, or confirm thepresence of a similar DNA or RNA in a particular cell or tissue.Oligonucleotides or oligomers comprise portions of a DNA sequence havingat least about 10 nucleotides and as many as about 35 nucleotides,preferably about 25 nucleotides.

“Probes” may be derived from naturally occurring or recombinant single-or double-stranded nucleic acids or may be chemically synthesized. Theyare useful in detecting the presence of identical or similar sequences.Such probes may be labeled with reporter molecules using nicktranslation, Klenow fill-in reaction, PCR or other methods well known inthe art. Nucleic acid probes may be used in southern, northern or insitu hybridizations to determine whether DNA or RNA encoding a certainprotein is present in a cell type, tissue, or organ.

A “fragment of a polynucleotide” is a nucleic acid that comprises all orany part of a given nucleotide molecule, the fragment having fewernucleotides than about 6 kb, preferably fewer than about 1 kb.

“Reporter molecules” are radionuclides, enzymes, fluorescent,chemiluminescent, or chromogenic agents which associate with aparticular nucleotide or amino acid sequence, thereby establishing thepresence of a certain sequence, or allowing for the quantification of acertain sequence.

“Chimeric” molecules may be constructed by introducing all or part ofthe nucleotide sequence of this invention into a vector containingadditional nucleic acid sequence which might be expected to change anyone or several of the following KLK9 characteristics: cellular location,distribution, ligand-binding affinities, interchain affinities,degradation/turnover rate, signaling, etc.

“Active”, with respect to a KLK9 polypeptide, refers to those forms,fragments, or domains of a KLK9 polypeptide which retain the biologicaland/or antigenic activity of a KLK9 polypeptide.

“Naturally occurring KLK9 polypeptide” refers to a polypeptide producedby cells which have not been genetically engineered and specificallycontemplates various polypeptides arising from post-translationalmodifications of the polypeptide including but not limited toacetylation, carboxylation, glycosylation, phos-phorylation, lipidationand acylation.

“Derivative” refers to polypeptides which have been chemically modifiedby techniques such as ubiquitination, labeling (see above), pegylation(derivatization with polyethylene glycol), and chemical insertion orsubstitution of amino acids such as ornithine which do not normallyoccur in human proteins.

“Conservative amino acid substitutions” result from replacing one aminoacid with another having similar structural and/or chemical properties,such as the replacement of a leucine with an isoleucine or valine, anaspartate with a glutamate, or a threonine with a serine.

“Insertions” or “deletions” are typically in the range of about 1 to 5amino acids. The variation allowed may be experimentally determined byproducing the peptide synthetically while systematically makinginsertions, deletions, or substitutions of nucleotides in the sequenceusing recombinant DNA techniques.

A “signal sequence” or “leader sequence” can be used, when desired, todirect the polypeptide through a membrane of a cell. Such a sequence maybe naturally present on the polypeptides of the present invention orprovided from heterologous sources by recombinant DNA techniques.

An “oligopeptide” is a short stretch of amino acid residues and may beexpressed from an oligonucleotide. Oligopeptides comprise a stretch ofamino acid residues of at least 3, 5, 10 amino acids and at most 10, 15,25 amino acids, typically of at least 9 to 13 amino acids, and ofsufficient length to display biological and/or antigenic activity.

“Inhibitor” is any substance which retards or prevents a chemical orphysiological reaction or response. Common inhibitors include but arenot limited to antisense molecules, antibodies, and antagonists.

“Standard expression” is a quantitative or qualitative measurement forcomparison. It is based on a statistically appropriate number of normalsamples and is created to use as a basis of comparison when performingdiagnostic assays, running clinical trials, or following patienttreatment profiles.

“Animal” as used herein may be defined to include human, domestic (e.g.,cats, dogs, etc.), agricultural (e.g., cows, horses, sheep, etc.) ortest species (e.g., mouse, rat, rabbit, etc.).

A “KLK9 polynucleotide”, within the meaning of the invention, shall beunderstood as being a nucleic acid molecule selected from a groupconsisting of

-   (i) nucleic acid molecules encoding a polypeptide comprising the    amino acid sequence of SEQ ID NO: 2,-   (ii) nucleic acid molecules comprising the sequence of SEQ ID NO: 1,-   (iii) nucleic acid molecules having the sequence of SEQ ID NO: 1,-   (iv) nucleic acid molecules the complementary strand of which    hybridizes under stringent conditions to a nucleic acid molecule of    (i), (ii), or (iii); and-   (v) nucleic acid molecules the sequence of which differs from the    sequence of a nucleic acid molecule of (iii) due to the degeneracy    of the genetic code;    wherein the polypeptide encoded by said nucleic acid molecule has    KLK9 activity.

A “KLK9 polypeptide”, within the meaning of the invention, shall beunderstood as being a polypeptide selected from a group consisting of

-   (i) polypeptides having the sequence of SEQ ID NO: 2,-   (ii) polypeptides comprising the sequence of SEQ ID NO: 2,-   (iii) polypeptides encoded by KLK9 polynucleotides; and-   (iv) polypeptides which show at least 99%, 98%, 95%, 90%, or 80%    homology with a polypeptide of (i), (ii), or (iii);    wherein said polypeptide has KLK9 activity.

The nucleotide sequences encoding a KLK9 (or their complement) havenumerous applications in techniques known to those skilled in the art ofmolecular biology. These techniques include use as hybridization probes,use in the construction of oligomers for PCR, use for chromosome andgene mapping, use in the recombinant production of KLK9, and use ingeneration of antisense DNA or RNA, their chemical analogs and the like.Uses of nucleotides encoding a KLK9 disclosed herein are exemplary ofknown techniques and are not intended to limit their use in anytechnique known to a person of ordinary skill in the art. Furthermore,the nucleotide sequences disclosed herein may be used in molecularbiology techniques that have not yet been developed, provided the newtechniques rely on properties of nucleotide sequences that are currentlyknown, e.g., the triplet genetic code, specific base pair interactions,etc.

It will be appreciated by those skilled in the art that as a result ofthe degeneracy of the genetic code, a multitude of KLK9—encodingnucleotide sequences may be produced. Some of these will only bearminimal homology to the nucleotide sequence of the known and naturallyoccurring KLK9. The invention has specifically contemplated each andevery possible variation of nucleotide sequence that could be made byselecting combinations based on possible codon choices. Thesecombinations are made in accordance with the standard triplet geneticcode as applied to the nucleotide sequence of naturally occurring KLK9,and all such variations are to be considered as being specificallydisclosed.

Although the nucleotide sequences which encode a KLK9, its derivativesor its variants are preferably capable of hybridizing to the nucleotidesequence of the naturally occurring KLK9 polynucleotide under stringentconditions, it may be advantageous to produce nucleotide sequencesencoding KLK9 polypeptides or its derivatives possessing a substantiallydifferent codon usage. Codons can be selected to increase the rate atwhich expression of the peptide occurs in a particular prokaryotic oreukaryotic expression host in accordance with the frequency with whichparticular codons are utilized by the host. Other reasons forsubstantially altering the nucleotide sequence encoding a KLK9polypeptide and/or its derivatives without altering the encoded aminoacid sequence include the production of RNA transcripts having moredesirable properties, such as a greater half-life, than transcriptsproduced from the naturally occurring sequence.

Nucleotide sequences encoding a KLK9 polypeptide may be joined to avariety of other nucleotide sequences by means of well establishedrecombinant DNA techniques. Useful nucleotide sequences for joining toKLK9 polynucleotides include an assortment of cloning vectors such asplasmids, cosmids, lambda phage derivatives, phagemids, and the like.Vectors of interest include expression vectors, replication vectors,probe generation vectors, sequencing vectors, etc. In general, vectorsof interest may contain an origin of replication functional in at leastone organism, convenient restriction endonuclease sensitive sites, andselectable markers for one or more host cell systems.

Another aspect of the subject invention is to provide for KLK9-specifichybridization probes capable of hybridizing with naturally occurringnucleotide sequences encoding KLK9. Such probes may also be used for thedetection of similar protease encoding sequences and should preferablyshow at least 40% nucleotide identity to KLK9 polynucleotides. Thehybridization probes of the subject invention may be derived from thenucleotide sequence presented as SEQ ID NO: 1 or from genomic sequencesincluding promoter, enhancers or introns of the native gene.Hybridization probes may be labelled by a variety of reporter moleculesusing techniques well known in the art.

It will be recognized that many deletional or mutational analogs of KLK9poly-nucleotides will be effective hybridization probes for KLK9polynucleotides. Accordingly, the invention relates to nucleic acidsequences that hybridize with such KLK9 encoding nucleic acid sequencesunder stringent conditions.

“Stringent conditions” refers to conditions that allow for thehybridization of substantially related nucleic acid sequences. Forinstance, such conditions will generally allow hybridization of sequencewith at least about 85% sequence identity, preferably with at leastabout 90% sequence identity, more preferably with at least about 95%sequence identity. Hybridization conditions and probes can be adjustedin well-characterized ways to achieve selective hybridization ofhuman-derived probes. Stringent conditions, within the meaning of theinvention are 65° C. in a buffer containing 1 mM EDTA, 0.5 M NaHPO₄ (H7.2), 7% (w/v) SDS.

Nucleic acid molecules that will hybridize to KLK9 polynucleotides understringent conditions can be identified functionally. Without limitation,examples of the uses for hybridization probes include: histochemicaluses such as identifying tissues that express KLK9; measuring mRNAlevels, for instance to identify a sample's tissue type or to identifycells that express abnormal levels of KLK9; and detecting poly-morphismsof KLK9.

PCR provides additional uses for oligonucleotides based upon thenucleotide sequence which encodes KLK9. Such probes used in PCR may beof recombinant origin, chemically synthesized, or a mixture of both.Oligomers may comprise discrete nucleotide sequences employed underoptimized conditions for identification of KLK9 in specific tissues ordiagnostic use. The same two oligomers, a nested set of oligomers, oreven a degenerate pool of oligomers may be employed under less stringentconditions for identification of closely related DNAs or RNAs.

Rules for designing polymerase chain reaction (PCR) primers are nowestablished, as reviewed by PCR Protocols. Degenerate primers, i.e.,preparations of primers that are heterogeneous at given sequencelocations, can be designed to amplify nucleic acid sequences that arehighly homologous to, but not identical with KLK9. Strategies are nowavailable that allow for only one of the primers to be required tospecifically hybridize with a known sequence. For example, appropriatenucleic acid primers can be ligated to the nucleic acid sought to beamplified to provide the hybridization partner for one of the primers.In this way, only one of the primers need be based on the sequence ofthe nucleic acid sought to be amplified.

PCR methods for amplifying nucleic acid will utilize at least twoprimers. One of these primers will be capable of hybridizing to a firststrand of the nucleic acid to be amplified and of priming enzyme-drivennucleic acid synthesis in a first direction. The other will be capableof hybridizing the reciprocal sequence of the first strand (if thesequence to be amplified is single stranded, this sequence willinitially be hypothetical, but will be synthesized in the firstamplification cycle) and of priming nucleic acid synthesis from thatstrand in the direction opposite the first direction and towards thesite of hybridization for the first primer. Conditions for conductingsuch amplifications, particularly under preferred stringenthybridization conditions, are well known.

Other means of producing specific hybridization probes for KLK9 includethe cloning of nucleic acid sequences encoding KLK9 or KLK9 derivativesinto vectors for the production of mRNA probes. Such vectors are knownin the art, are commercially available and may be used to synthesize RNAprobes in vitro by means of the addition of the appropriate RNApolymerase as T7 or SP6 RNA polymerase and the appropriate reportermolecules.

It is possible to produce a DNA sequence, or portions thereof, entirelyby synthetic chemistry. After synthesis, the nucleic acid sequence canbe inserted into any of the many available DNA vectors and theirrespective host cells using techniques which are well known in the art.Moreover, synthetic chemistry may be used to introduce mutations intothe nucleotide sequence. Alternately, a portion of sequence in which amutation is desired can be synthesized and recombined with longerportion of an existing genomic or recombinant sequence.

KLK9 polynucleotides may be used to produce a purified oligo-orpolypeptide using well known methods of recombinant DNA technology. Theoligopeptide may be expressed in a variety of host cells, eitherprokaryotic or eukaryotic. Host cells may be from the same species fromwhich the nucleotide sequence was derived or from a different species.Advantages of producing an oligonucleotide by recombinant DNA technologyinclude obtaining adequate amounts of the protein for purification andthe availability of simplified purification procedures.

Quantitative determinations of nucleic acids

An important step in the molecular genetic analysis of human disease isoften the enumeration of the copy number of a nucleis acid or therelative expression of a gene in particular tissues. Several differentapproaches are currently available to make quantitative deter-minationsof nucleic acids. Chromosome-based techniques, such as comparativegenomic hybridization (CGH) and fluorescent in situ hybridization (FISH)facilitate efforts to cytogenetically localize genomic regions that arealtered in tumor cells.

Regions of genomic alteration can be narrowed further using loss ofheterozygosity analysis (LOH), in which disease DNA is analyzed andcompared with normal DNA for the loss of a heterozygous polymorphicmarker. The first experiments used restriction fragment lengthpolymorphisms (RFLPs) [Johnson, (1989)], or hyper-variable minisatelliteDNA [Barnes, 2000]. In recent years LOH has been performed primarilyusing PCR amplification of microsatellite markers and electrophoresis ofthe radio labelled [Jeffreys, (1985)] or fluorescently labelled PCRproducts [Weber, (1990)] and compared between paired normal and diseaseDNAs.

A number of other methods have also been developed to quantify nucleicacids [Gergen, (1992)]. More recently, PCR and RT-PCR methods have beendeveloped which are capable of measuring the amount of a nucleic acid ina sample. One approach, for example, measures PCR product quantity inthe log phase of the reaction before the formation of reaction productsplateaus [Thomas, (1980)].

A gene sequence contained in all samples at relatively constant quantityis typically utilized for sample amplification efficiency normalization.This approach, however, suffers from several drawbacks. The methodrequires that each sample has equal input amounts of the nucleic acidand that the amplification efficiency between samples is identical untilthe time of analysis. Furthermore, it is difficult using theconventional methods of PCR quantitation such as gel electrophoresis orplate capture hybridization to determine that all samples are in factanalyzed during the log phase of the reaction as required by the method.

Another method called quantitative competitive (QC)-PCR, as the nameimplies, relies on the inclusion of an internal control competitor ineach reaction [Piatak, (1993), BioTechniques]. The efficiency of eachreaction is normalized to the internal competitor. A known amount ofinternal competitor is typically added to each sample. The unknowntarget PCR product is compared with the known competitor PCR product toobtain relative quantitation. A difficulty with this general approachlies in developing an internal control that amplifies with the sameefficiency than the target molecule.

5′ Fluorogenic Nuclease Assays

Fluorogenic nuclease assays are a real time quantitation method thatuses a probe to monitor formation of amplification product. The basisfor this method of monitoring the formation of amplification product isto measure continuously PCR product accumulation using a dual-labelledfluorogenic oligonucleotide probe, an approach frequently referred to inthe literature simply as the “TaqMan method” [Piatak,(1993), Science;Heid, (1996); Gibson, (1996); Holland. (1991)].

The probe used in such assays is typically a short (about 20-25 bases)oligonucleotide that is labeled with two different fluorescent dyes. The5′ terminus of the probe is attached to a reporter dye and the 3′terminus is attached to a quenching dye, although the dyes could beattached at other locations on the probe as well. The probe is designedto have at least substantial sequence complementarity with the probebinding site. Upstream and downstream PCR primers which bind to flankingregions of the locus are added to the reaction mixture. When the probeis intact, energy transfer between the two fluorophors occurs and thequencher quenches emission from the reporter. During the extension phaseof PCR, the probe is cleaved by the 5′ nuclease activity of a nucleicacid polymerase such as Taq polymerase, thereby releasing the reporterfrom the oligonucleotide-quencher and resulting in an increase ofreporter emission intensity which can be measured by an appropriatedetector.

One detector which is specifically adapted for measuring fluorescenceemissions such as those created during a fluorogenic assay is the ABI7700 or 4700 HT manufactured by Applied Biosystems, Inc. in Foster City,Calif. The ABI 7700 uses fiber optics connected with each well in a96-or 384 well PCR tube arrangement. The instrument includes a laser forexciting the labels and is capable of measuring the fluorescence spectraintensity from each tube with continuous monitoring during PCRamplification. Each tube is re-examined every 8.5 seconds.

Computer software provided with the instrument is capable of recordingthe fluorescence intensity of reporter and quencher over the course ofthe amplification. The recorded values will then be used to calculatethe increase in normalized reporter emission intensity on a continuousbasis. The increase in emission intensity is plotted versus time, i.e.,the number of amplification cycles, to produce a continuous measure ofamplification. To quantify the locus in each amplification reaction, theamplification plot is examined at a point during the log phase ofproduct accumulation. This is accomplished by assigning a fluorescencethreshold intensity above background and determining the point at whicheach amplification plot crosses the threshold (defined as the thresholdcycle number or Ct). Differences in threshold cycle number are used toquantify the relative amount of PCR target contained within each tube.Assuming that each reaction functions at 100% PCR efficiency, adifference of one Ct represents a two-fold difference in the amount ofstarting template. The fluorescence value can be used in conjunctionwith a standard curve to determine the amount of amplification productpresent.

Non-Probe-Based Detection Methods

A variety of options are available for measuring the amplificationproducts as they are formed. One method utilizes labels, such as dyes,which only bind to double stranded DNA. In this type of approach,amplification product (which is double stranded) binds dye molecules insolution to form a complex. With the appropriate dyes, it is possible todistinguish between dye molecules free in solution and dye moleculesbound to amplification product. For example, certain dyes fluoresce onlywhen bound to amplification product. Examples of dyes which can be usedin methods of this general type include, but are not limited to, SyberGreen™ and Pico Green from Molecular Probes, Inc. of Eugene, Oreg.,ethidium bromide, propidium iodide, chromomycin, acridine orange,Hoechst 33258, Toto-1, Yoyo-1, DAPI (4′,6-diamidino-2-phenylindolehydrochloride).

Another real time detection technique measures alteration in energyfluorescence energy transfer between fluorophors conjugated with PCRprimers [Livak, (1995)].

Probe-Based Detection Methods

These detection methods involve some alteration to the structure orconformation of a probe hybridized to the locus between theamplification primer pair. In some instances, the alteration is causedby the template-dependent extension catalyzed by a nucleic acidpolymerase during the amplification process. The alteration generates adetectable signal which is an indirect measure of the amount ofamplification product formed.

For example, some methods involve the degradation or digestion of theprobe during the extension reaction. These methods are a consequence ofthe 5′-3′ nuclease activity associated with some nucleic acidpolymerases. Polymerases having this activity cleave mononucleotides orsmall oligonucleotides from an oligonucleotide probe annealed to itscomplementary sequence located within the locus.

The 3′ end of the upstream primer provides the initial binding site forthe nucleic acid polymerase. As the polymerase catalyzes extension ofthe upstream primer and encounters the bound probe, the nucleic acidpolymerase displaces a portion of the 5′ end of the probe and throughits nuclease activity cleaves mononucleotides or oligonucleotides fromthe probe.

The upstream primer and the probe can be designed such that they annealto the complementary strand in close proximity to one another. In fact,the 3′ end of the upstream primer and the 5′ end of the probe may abutone another. In this situation, extension of the upstream primer is notnecessary in order for the nucleic acid polymerase to begin cleaving theprobe. In the case in which intervening nucleotides separate theupstream primer and the probe, extension of the primer is necessarybefore the nucleic acid polymerase encounters the 5′ end of the probe.Once contact occurs and polymerization continues, the 5′-3′ exonucleaseactivity of the nucleic acid polymerase begins cleaving mononucleotidesor oligonucleotides from the 5′ end of the probe. Digestion of the probecontinues until the remaining portion of the probe dissociates from thecomplementary strand.

In solution, the two end sections can hybridize with each other to forma hairpin loop. In this conformation, the reporter and quencher dye arein sufficiently close proximity that fluorescence from the reporter dyeis effectively quenched by the quencher dye. Hybridized probe, incontrast, results in a linearized conformation in which the extent ofquenching is decreased. Thus, by monitoring emission changes for the twodyes, it is possible to indirectly monitor the formation ofamplification product.

Probes

The labeled probe is selected so that its sequence is substantiallycomplementary to a segment of the test locus or a reference locus. Asindicated above, the nucleic acid site to which the probe binds shouldbe located between the primer binding sites for the upstream anddownstream amplification primers.

Primers

The primers used in the amplification are selected so as to be capableof hybridizing to sequences at flanking regions of the locus beingamplified. The primers are chosen to have at least substantialcomplementarity with the different strands of the nucleic acid beingamplified. When a probe is utilized to detect the formation ofamplification products, the primers are selected in such that they flankthe probe, i.e. are located upstream and downstream of the probe.

The primer must have sufficient length so that it is capable of primingthe synthesis of extension products in the presence of an agent forpolymerization. The length and composition of the primer depends on manyparameters, including, for example, the temperature at which theannealing reaction is conducted, proximity of the probe binding site tothat of the primer, relative concentrations of the primer and probe andthe particular nucleic acid composition of the probe. Typically theprimer includes 15-30 nucleotides. However, the length of the primer maybe more or less depending on the complexity of the primer binding siteand the factors listed above.

Labels for Probes and Primers

The labels used for labeling the probes or primers of the currentinvention and which can provide the signal corresponding to the quantityof amplification product can take a variety of forms. As indicated abovewith regard to the 5′ fluorogenic nuclease method, a fluorescent signalis one signal which can be measured. However, measurements may also bemade, for example, by monitoring radioactivity, colorimetry, absorption,magnetic parameters, or enzymatic activity. Thus, labels which can beemployed include, but are not limited to, fluorophors, chromophores,radioactive isotopes, electron dense reagents, enzymes, and ligandshaving specific binding partners (e.g., biotin-avidin).

Monitoring changes in fluorescence is a particularly useful way tomonitor the accumulation of amplification products. A number of labelsuseful for attachment to probes or primers are commercially availableincluding fluorescein and various fluorescein derivatives such as FAM,HEX, TET and JOE (all which are available from Applied Biosystems,Foster City, Calif.); lucifer yellow, and coumarin derivatives.

Labels may be attached to the probe or primer using a variety oftechniques and can be attached at the 5′ end, and/or the 3′ end and/orat an internal nucleotide. The label can also be attached to spacer armsof various sizes which are attached to the probe or primer. These spacerarms are useful for obtaining a desired distance between multiple labelsattached to the probe or primer.

In some instances, a single label may be utilized; whereas, in otherinstances, such as with the 5′ fluorogenic nuclease assays for example,two or more labels are attached to the probe. In cases wherein the probeincludes multiple labels, it is generally advisable to maintain spacingbetween the labels which is sufficient to permit separation of thelabels during digestion of the probe through the 5′-3′ nuclease activityof the nucleic acid polymerase.

Patients Exhibiting Symptoms of Disease

A number of diseases are associated with changes in the copy number of acertain gene. For patients having symptoms of a disease, the real-timePCR method can be used to determine if the patient has copy numberalterations which are known to be linked with diseases that areassociated with the symptoms the patient has.

KLK9 Expression

KLK9 Fusion Proteins

Fusion proteins are useful for generating antibodies against KLK9polypeptides and for use in various assay systems. For example, fusionproteins can be used to identify proteins which interact with portionsof KLK9 polypeptides. Protein affinity chromatography or library-basedassays for protein-protein interactions, such as the yeast two-hybrid orphage display systems, can be used for this purpose. Such methods arewell known in the art and also can be used as drug screens.

A KLK9 fusion protein comprises two polypeptide segments fused togetherby means of a peptide bond. The first polypeptide segment can compriseat least 54, 75, 100, 125, 139, 150, 175, 200, 225, 250, 275, 300, 325or 350 contiguous amino acids of SEQ ID NO: 2 or of a biologicallyactive variant, such as those described above. The first polypeptidesegment also can comprise full-length KLK9.

The second polypeptide segment can be a full-length protein or a proteinfragment. Proteins commonly used in fusion protein construction include,but are not limited to β galactosidase, β-glucuronidase, greenfluorescent protein (GFP), autofluorescent proteins, including bluefluorescent protein (BFP), glutathione-S-transferase (GST), luciferase,horseradish peroxidase (HRP), and chloramphenicol acetyltransferase(CAT). Additionally, epitope tags are used in fusion proteinconstructions, including histidine (His) tags, FLAG tags, influenzahemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx)tags. Other fusion constructions can include maltose binding protein(MBP), S-tag, Lex a DNA binding domain (DBD) fusions, GAL4 DNA bindingdomain fusions, and herpes simplex virus (HSV) BP16 protein fusions. Afusion protein also can be engineered to contain a cleavage site locatedadjacent to the KLK9.

Preparation of Polynucleotides

A naturally occurring KLK9 polynucleotide can be isolated free of othercellular components such as membrane components, proteins, and lipids.Polynucleotides can be made by a cell and isolated using standardnucleic acid purification techniques, or synthesized using anamplification technique, such as the polymerase chain reaction (PCR), orby using an automatic synthesizer. Methods for isolating polynucleotidesare routine and are known in the art. Any such technique for obtaining apolynucleotide can be used to obtain isolated KLK9 polynucleotides. Forexample, restriction enzymes and probes can be used to isolatepolynucleotide fragments which comprise KLK9 nucleotide sequences.Isolated polynucleotides are in preparations which are free or at least70, 80, or 90% free of other molecules.

KLK9 cDNA molecules can be made with standard molecular biologytechniques, using KLK9 mRNA as a template. KLK9 cDNA molecules canthereafter be replicated using molecular biology techniques known in theart. An amplification technique, such as PCR, can be used to obtainadditional copies of polynucleotides of the invention, using eitherhuman genomic DNA or cDNA as a template.

Alternatively, synthetic chemistry techniques can be used to synthesizesKLK9 polynucleotides. The degeneracy of the genetic code allowsalternate nucleotide sequences to be synthesized which will encode KLK9having, for example, an amino acid sequence shown in SEQ ID NO: 2 or abiologically active variant thereof.

Extending Polynucleotides

Various PCR-based methods can be used to extend nucleic acid sequencesencoding human KLK9, for example to detect upstream sequences of KLK9gene such as promoters and regulatory elements. For example,restriction-site PCR uses universal primers to retrieve unknown sequenceadjacent to a known locus. Genomic DNA is first amplified in thepresence of a primer to a linker sequence and a primer specific to theknown region. The amplified sequences are then subjected to a secondround of PCR with the same linker primer and another specific primerinternal to the first one. Products of each round of PCR are transcribedwith an appropriate RNA polymerase and sequenced using reversetranscriptase.

Inverse PCR also can be used to amplify or extend sequences usingdivergent primers based on a known region. Primers can be designed usingcommercially available software, such as OLIGO 4.06 Primer Analysissoftware (National Biosciences Inc., Plymouth, Minn.), to be 22-30nucleotides in length, to have a GC content of 50% or more, and toanneal to the target sequence at temperatures about 68-72° C. The methoduses several restriction enzymes to generate a suitable fragment in theknown region of a gene. The fragment is then circularized byintramolecular ligation and used as a PCR template.

Another method which can be used is capture PCR, which involves PCRamplification of DNA fragments adjacent to a known sequence in human andyeast artificial chromosome DNA. In this method, multiple restrictionenzyme digestions and ligations also can be used to place an engineereddouble-stranded sequence into an unknown fragment of the DNA moleculebefore performing PCR.

When screening for full-length cDNAs, it is preferable to use librariesthat have been size-selected to include larger cDNAs. Randomly-primedlibraries are preferable, in that they will contain more sequences whichcontain the 5′ regions of genes. Use of a randomly primed library may beespecially preferable for situations in which an oligo d(T) library doesnot yield a full-length cDNA. Genomic libraries can be useful forextension of sequence into 5′ non-transcribed regulatory regions.

Commercially available capillary electrophoresis systems can be used toanalyze the size or confirm the nucleotide sequence of PCR or sequencingproducts. For example, capillary sequencing can employ flowable polymersfor electrophoretic separation, four different fluorescent dyes (one foreach nucleotide) which are laser activated, and detection of the emittedwavelengths by a charge coupled device camera. Output/light intensitycan be converted to electrical signal using appropriate equipment andsoftware (e.g., GENOTYPER and Sequence NAVIGATOR, Perkin Elmer), and theentire process from loading of samples to computer analysis andelectronic data display can be computer controlled. Capillaryelectrophoresis is especially preferable for the sequencing of smallpieces of DNA which might be present in limited amounts in a particularsample.

Obtaining Polypeptides

KLK9 can be obtained, for example, by purification from human cells, byexpression of KLK9 polynucleotides, or by direct chemical synthesis.

Protein Purification

KLK9 can be purified from any human cell which expresses the enzyme,including those which have been transfected with expression constructswhich express KLK9. A purified KLK9 is separated from other compoundswhich normally associate with KLK9 in the cell, such as certainproteins, carbohydrates, or lipids, using methods well-known in the art.Such methods include, but are not limited to, size exclusionchromatography, ammonium sulfate fractionation, ion exchangechromatography, affinity chromatography, and preparative gelelectrophoresis.

Expression of KLK9 Polynucleotides

To express KLK9, KLK9 polynucleotides can be inserted into an expressionvector which contains the necessary elements for the transcription andtranslation of the inserted coding sequence. Methods which are wellknown to those skilled in the art can be used to construct expressionvectors containing sequences encoding KLK9 and appropriatetranscriptional and translational control elements. These methodsinclude in vitro recombinant DNA techniques, synthetic techniques, andin vivo genetic recombination.

A variety of expression vector/host systems can be utilized to containand express sequences encoding KLK9. These include, but are not limitedto, microorganisms, such as bacteria transformed with recombinantbacteriophage, plasmid, or cosmid DNA expression vectors; yeasttransformed with yeast expression vectors, insect cell systems infectedwith virus expression vectors (e.g., baculovirus), plant cell systemstransformed with virus expression vectors (e.g., cauliflower mosaicvirus, CaMV; tobacco mosaic virus, TMV) or with bacterial expressionvectors (e.g., Ti or pBR322 plasmids), or animal cell systems.

The control elements or regulatory sequences are those non-translatedregions of the vector—enhancers, promoters, S′ and 3′ untranslatedregions—which interact with host cellular proteins to carry outtranscription and translation. Such elements can vary in their strengthand specificity. Depending on the vector system and host utilized, anynumber of suitable transcription and translation elements, includingconstitutive and inducible promoters, can be used. For example, whencloning in bacterial systems, inducible promoters such as the hybridlacZ promoter of the BLUESCRIPT phagemid (Stratagene, LaJolla, Calif.)or pSPORT1 plasmid (Life Technologies) and the like can be used. Thebaculovirus polyhedrin promoter can be used in insect cells. Promotersor enhancers derived from the genomes of plant cells (e.g., heat shock,RUBISCO, and storage protein genes) or from plant viruses (e.g., viralpromoters or leader sequences) can be cloned into the vector. Inmammalian cell systems, promoters from mammalian genes or from mammalianviruses are preferable. If it is necessary to generate a cell line thatcontains multiple copies of a nucleotide sequence encoding KLK9, vectorsbased on SV40 or EBV can be used with an appropriate selectable marker.

Bacterial and Yeast Expression Systems

In bacterial systems, a number of expression vectors can be selected.For example, when a large quantity of KLK9 is needed for the inductionof antibodies, vectors which direct high level expression of fusionproteins that are readily purified can be used. Such vectors include,but are not limited to, multifunctional E. coli cloning and expressionvectors such as BLUESCRIPT (Stratagene). In a BLUESCRIPT vector, asequence encoding KLK9 can be ligated into the vector in frame withsequences for the amino-terminal Met and the subsequent 7 residues ofβ-galactosidase so that a hybrid protein is produced. pIN vectors orpGEX vectors (Promega, Madison, Wis.) also can be used to expressforeign polypeptides as fusion proteins with glutathione S-transferase(GST). In general, such fusion proteins are soluble and can easily bepurified from lysed cells by adsorption to glutathione-agarose beadsfollowed by elution in the presence of free glutathione. Proteins madein such systems can be designed to include heparin, thrombin, or factorXa protease cleavage sites so that the cloned polypeptide of interestcan be released from the GST moiety at will.

Plant and Insect Expression Systems

If plant expression vectors are used, the expression of sequencesencoding KLK9 can be driven by any of a number of promoters. Forexample, viral promoters such as the 35S and 19S promoters of CaMV canbe used alone or in combination with the omega leader sequence from TMV.Alternatively, plant promoters such as the small subunit of RUBISCO orheat shock promoters can be used. These constructs can be introducedinto plant cells by direct DNA transformation or by pathogen-mediatedtransfection.

An insect system also can be used to express KLK9. For example, in onesuch system Autographa californica nuclear polyhedrosis virus (AcNPV) isused as a vector to express foreign genes in Spodoptera frugiperda cellsor in Trichoplusia larvae. Sequences encoding KLK9 can be cloned into anon-essential region of the virus, such as the polyhedrin gene, andplaced under control of the polyhedrin promoter. Successful insertion ofKLK9 will render the polyhedrin gene inactive and produce recombinantvirus lacking coat protein. The recombinant viruses can then be used toinfect S. frugiperda cells or Trichoplusia larvae in which KLK9 can beexpressed.

Mammalian Expression Systems

A number of viral-based expression systems can be used to express KLK9in mammalian host cells. For example, if an adenovirus is used as anexpression vector, sequences encoding KLK9 can be ligated into anadenovirus transcription/translation complex comprising the latepromoter and tripartite leader sequence. Insertion in a non-essential E1or E3 region of the viral genome can be used to obtain a viable viruswhich is capable of expressing KLK9 in infected host cells [Engelhard,1994)]. If desired, transcription enhancers, such as the Rous sarcomavirus (RSV) enhancer, can be used to increase expression in mammalianhost cells.

Human artificial chromosomes (HACs) also can be used to deliver largerfragments of DNA than can be contained and expressed in a plasmid. HACsof 6M to 10M are constructed and delivered to cells via conventionaldelivery methods (e.g., liposomes, polycationic amino polymers, orvesicles). Specific initiation signals also can be used to achieve moreefficient translation of sequences encoding KLK9. Such signals includethe ATG initiation codon and adjacent sequences. In cases wheresequences encoding KLK9, its initiation codon, and upstream sequencesare inserted into the appropriate expression vector, no additionaltranscriptional or translational control signals may be needed. However,in cases where only coding sequence, or a fragment thereof, is inserted,exogenous translational control signals (including the ATG initiationcodon) should be provided. The initiation codon should be in the correctreading frame to ensure translation of the entire insert. Exogenoustranslational elements and initiation codons can be of various origins,both natural and synthetic.

Host Cells

A host cell strain can be chosen for its ability to modulate theexpression of the inserted sequences or to process the expressed KLK9 inthe desired fashion. Such modifications of the polypeptide include, butare not limited to, acetylation, carboxylation, glycosylation,phosphorylation, lipidation, and acylation. Post-translationalprocessing which cleaves a “prepro” form of the polypeptide also can beused to facilitate correct insertion, folding and/or function. Differenthost cells which have specific cellular machinery and characteristicmechanisms for post-translational activities (e.g., CHO, HeLa, MDCK,HEK293, and WI38), are available from the American Type CultureCollection (ATCC; 10801 University Boulevard, Manassas, Va. 20110-2209)and can be chosen to ensure the correct modification and processing ofthe foreign protein.

Stable expression is preferred for long-term, high-yield production ofrecombinant proteins. For example, cell lines which stably express KLK9can be transformed using expression vectors which can contain viralorigins of replication and/or endogenous expression elements and aselectable marker gene on the same or on a separate vector. Followingthe introduction of the vector, cells can be allowed to grow for 1-2days in an enriched medium before they are switched to a selectivemedium. The purpose of the selectable marker is to confer resistance toselection, and its presence allows growth and recovery of cells whichsuccessfully express the introduced KLK9 sequences. Resistant clones ofstably transformed cells can be proliferated using tissue culturetechniques appropriate to the cell type. Any number of selection systemscan be used to recover transformed cell lines. These include, but arenot limited to, the herpes simplex virus thymidine kinase [Logan,(1984)] and adenine phosphoribosyltransferase [Wigler, (1977)] geneswhich can be employed in t k or apr f cells, respectively. Also,antimetabolite, antibiotic, or herbicide resistance can be used as thebasis for selection. For example, dhfr confers resistance tomethotrexate [Lowy, (1980)], npt confers resistance to theaminoglycosides, neomycin and G-418 [Wigler, (1980)], and als and patconfer resistance to chlorsulfuron and phosphinotricinacetyltransferase, respectively [Colbere-Garapin, 1981]. Additionalselectable genes have been described. For example, trpB allows cells toutilize indole in place of tryptophan, or hisD, which allows cells toutilize histinol in place of histidine. Visible markers such asanthocyanins, β-glucuronidase and its substrate GUS, and luciferase andits substrate luciferin, can be used to identify transformants and toquantify the amount of transient or stable protein expressionattributable to a specific vector system

Detecting Polypeptide Expression

Although the presence of marker gene expression suggests that a KLK9poly-nucleotide is also present, its presence and expression may need tobe confirmed. For example, if a sequence encoding KLK9 is insertedwithin a marker gene sequence, transformed cells containing sequenceswhich encode KLK9 can be identified by the absence of marker genefunction. Alternatively, a marker gene can be placed in tandem with asequence encoding KLK9 under the control of a single promoter.Expression of the marker gene in response to induction or selectionusually indicates expression of KLK9 polynucleotide.

Alternatively, host cells which contain a KLK9 polynucleotide and whichexpress KLK9 can be identified by a variety of procedures known to thoseof skill in the art. These procedures include, but are not limited to,DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassaytechniques which include membrane, solution, or chip-based technologiesfor the detection and/or quantification of nucleic acid or protein. Forexample, the presence of a polynucleotide sequence encoding KLK9 can bedetected by DNA-DNA or DNA-RNA hybridization or amplification usingprobes or fragments or fragments of polynucleotides encoding KLK9.Nucleic acid amplification-based assays involve the use ofoligonucleotides selected from sequences encoding KLK9 to detecttransformants which contain a KLK9 polynucleotide.

A variety of protocols for detecting and measuring the expression ofKLK9, using either polyclonal or monoclonal antibodies specific for thepolypeptide, are known in the art. Examples include enzyme-linkedimmunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescenceactivated cell sorting (FACS). A two-site, monoclonal-based immunoassayusing monoclonal antibodies reactive to two non-interfering epitopes onKLK9 can be used, or a competitive binding assay can be employed.

A wide variety of labels and conjugation techniques are known by thoseskilled in the art and can be used in various nucleic acid and aminoacid assays. Means for producing labeled hybridization or PCR probes fordetecting sequences related to polynucleotides encoding KLK9 includeoligolabeling, nick translation, end-labeling, or PCR amplificationusing a labeled nucleotide. Alternatively, sequences encoding KLK9 canbe cloned into a vector for the production of an mRNA probe. Suchvectors are known in the art, are commercially available, and can beused to synthesize RNA probes in vitro by addition of labelednucleotides and an appropriate RNA polymerase such as T7, T3, or SP6.These procedures can be conducted using a variety of commerciallyavailable kits (Amersham Pharmacia Biotech, Promega, and USBiochemical). Suitable reporter molecules or labels which can be usedfor ease of detection include radionuclides, enzymes, and fluorescent,chemiluminescent, or chromogenic agents, as well as substrates,cofactors, inhibitors, magnetic particles, and the like.

Expression and Purification of Polypeptides

Host cells transformed with KLK9 polynucleotides can be cultured underconditions suitable for the expression and recovery of the protein fromcell culture. The poly-peptide produced by a transformed cell can besecreted or contained intracellularly depending on the sequence and/orthe vector used. As will be understood by those of skill in the art,expression vectors containing KLK9 polynucleotides can be designed tocontain signal sequences which direct secretion of soluble KLK9 througha prokaryotic or eukaryotic cell membrane or which direct the membraneinsertion of membrane-bound KLK9.

As discussed above, other constructions can be used to join a sequenceencoding KLK9 to a nucleotide sequence encoding a polypeptide domainwhich will facilitate purification of soluble proteins. Suchpurification facilitating domains include, but are not limited to, metalchelating peptides such as histidine-tryptophan modules that allowpurification on immobilized metals, protein A domains that allowpurification on immobilized immunoglobulin, and the domain utilized inthe FLAGS extension/affinity purification system (Immunex Corp.,Seattle, Wash.). Inclusion of cleavable linker sequences such as thosespecific for Factor XA or enterokinase (Invitrogen, San Diego, Calif.)between the purification domain and KLK9 also can be used to facilitatepurification. One such expression vector provides for expression of afusion protein containing KLK9 and 6 histidine residues preceding athioredoxin or an enterokinase cleavage site. The histidine residuesfacilitate purification by IMAC (immobilized metal ion affinitychromatography) Maddox, (1983)], while the enterokinase cleavage siteprovides a means for purifying KLK9 from the fusion protein [Porath,(1992)].

Chemical Synthesis

Sequences encoding KLK9 can be synthesized, in whole or in part, usingchemical methods well known in the art. Alternatively, KLK9 itself canbe produced using chemical methods to synthesize its amino acidsequence, such as by direct peptide synthesis using solid-phasetechniques. Protein synthesis can either be performed using manualtechniques or by automation. Automated synthesis can be achieved, forexample, using Applied Biosystems 431A Peptide Synthesizer (PerkinElmer). Optionally, fragments of KLK9 can be separately synthesized andcombined using chemical methods to produce a full-length molecule.

The newly synthesized peptide can be substantially purified bypreparative high performance liquid chromatography. The composition of asynthetic KLK9 can be confirmed by amino acid analysis or sequencing.Additionally, any portion of the amino acid sequence of KLK9 can bealtered during direct synthesis and/or combined using chemical methodswith sequences from other proteins to produce a variant polypeptide or afusion protein.

Production of Altered Polypeptides

As will be understood by those of skill in the art, it may beadvantageous to produce KLK9 polynucleotides possessing non-naturallyoccurring codons. For example, codons preferred by a particularprokaryotic or eukaryotic host can be selected to increase the rate ofprotein expression or to produce an RNA transcript having desirableproperties, such as a half-life which is longer than that of atranscript generated from the naturally occurring sequence.

The nucleotide sequences referred to herein can be engineered usingmethods generally known in the art to alter KLK9 polynucleotides for avariety of reasons, including but not limited to, alterations whichmodify the cloning, processing, and/or expression of the polypeptide ormRNA product. DNA shuffling by random fragmentation and PCR reassemblyof gene fragments and synthetic oligonucleotides can be used to engineerthe nucleotide sequences. For example, site-directed mutagenesis can beused to insert new restriction sites, alter glycosylation patterns,change codon preference, produce splice variants, introduce mutations,and so forth.

KLK9 Analogs

One general class of KLK9 analogs are variants having an amino acidsequence that is a mutation of the amino acid sequence disclosed herein.Another general class of KLK9 analogs is provided by anti-idiotypeantibodies, and fragments thereof, as described below. Moreover,recombinant antibodies comprising anti-idiotype variable domains can beused as analogs (see, for example, [Monfardini et al., (1996)]). Sincethe variable domains of anti-idiotype KLK9 antibodies mimic KLK9, thesedomains can provide KLK9 enzymatic activity. Methods of producinganti-idiotypic catalytic antibodies are known to those of skill in theart [Joron et al., (1992), Friboulet et al. (1994), Avalle et al.,(1998)].

Another approach to identifying KLK9 analogs is provided by the use ofcombinatorial libraries. Methods for constructing and screening phagedisplay and other combinatorial libraries are provided, for example, by[Kay et al., Phage Display of Peptides and Proteins (Academic Press1996), U.S. Pat. Nos. 5,783,384, 5,747,334, and 5,723,323.

One illustrative in vitro use of KLK9 and its analogs is the productionof labeled peptides from a labeled protein substrate. Proteases can alsobe used in detergents and cleaning solutions. For example, serineproteases are used in solutions to clean and to disinfect contact lenses(see, for example, [U.S. Pat. No. 5,985,629]). Another use for a serineprotease is in the formulation of vaccines (see, for example, [U.S.5,885,814]). Those of skill in the art can devise other uses formolecules having KLK9 activity.

Antibodies

Any type of antibody known in the art can be generated to bindspecifically to an epitope of KLK9.

“Antibody” as used herein includes intact immunoglobulin molecules, aswell as fragments thereof, such as Fab, F(ab′)₂, and Fv, which arecapable of binding an epitope of KLK9. Typically, at least 6, 8, 10, or12 contiguous amino acids are required to form an epitope. However,epitopes which involve non-contiguous amino acids may require more,e.g., at least 15, 25, or 50 amino acid. An antibody which specificallybinds to an epitope of KLK9 can be used therapeutically, as well as inimmunochemical assays, such as Western blots, ELISAs, radioimmunoassays,immunohistochemical assays, immunoprecipitations, or otherimmunochemical assays known in the art. Various immunoassays can be usedto identify antibodies having the desired specificity. Numerousprotocols for competitive binding or immunoradiometric assays are wellknown in the art. Such immunoassays typically involve the measurement ofcomplex formation between an immunogen and an antibody whichspecifically binds to the KLK9 immunogen.

Typically, an antibody which specifically binds to KLK9 provides adetection signal at least 5-, 10-, or 20-fold higher than a detectionsignal provided with other proteins when used in an immunochemicalassay. Preferably, antibodies which specifically bind to KLK9 do notdetect other proteins in immunochemical assays and can immunoprecipitateKLK9 from solution.

KLK9 can be used to immunize a mammal, such as a mouse, rat, rabbit,guinea pig, monkey, or human, to produce polyclonal antibodies. Ifdesired, KLK9 can be conjugated to a carrier protein, such as bovineserum albumin, thyroglobulin, and keyhole limpet hemocyanin. Dependingon the host species, various adjuvants can be used to increase theimmunological response. Such adjuvants include, but are not limited to,Freund's adjuvant, mineral gels (e.g., aluminum hydroxide), and surfaceactive substances (e.g., lysolecithin, pluronic polyols, polyanions,peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol).Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) andCorynebacterium parvum are especially useful.

Monoclonal antibodies which specifically bind to KLK9 can be preparedusing any technique which provides for the production of antibodymolecules by continuous cell lines in culture. These techniques include,but are not limited to, the hybridoma technique, the human B-cellhybridoma technique, and the EBV-hybridoma technique [Roberge, (1995)].

In addition, techniques developed for the production of “chimericantibodies”, the splicing of mouse antibody genes to human antibodygenes to obtain a molecule with appropriate antigen specificity andbiological activity, can be used. Monoclonal and other antibodies alsocan be “humanized” to prevent a patient from mounting an immune responseagainst the antibody when it is used therapeutically. Such antibodiesmay be sufficiently similar in sequence to human antibodies to be useddirectly in therapy or may require alteration of a few key residues.Sequence differences between rodent antibodies and human sequences canbe minimized by replacing residues which differ from those in the humansequences by site directed mutagenesis of individual residues or bygrating of entire complementarity determining regions. Antibodies whichspecifically bind to KLK9 can contain antigen binding sites which areeither partially or fully humanized, as disclosed in U.S. Pat. No.5,565,332.

Alternatively, techniques described for the production of single chainantibodies can be adapted using methods known in the art to producesingle chain antibodies which specifically bind to KLK9. Antibodies withrelated specificity, but of distinct idiotypic composition, can begenerated by chain shuffling from random combinatorial immunoglobinlibraries. Single-chain antibodies also can be constructed using a DNAamplification method, such as PCR, using hybridoma cDNA as a template.Single-chain antibodies can be mono- or bispecific, and can be bivalentor tetravalent. Construction of tetravalent, bispecific single-chainantibodies is taught. A nucleotide sequence encoding a single-chainantibody can be constructed using manual or automated nucleotidesynthesis, cloned into an expression construct using standardrecombinant DNA methods, and introduced into a cell to express thecoding sequence, as described below. Alternatively, single-chainantibodies can be produced directly using, for example, filamentousphage technology.

Antibodies which specifically bind to KLK9 also can be produced byinducing in vivo production in the lymphocyte population or by screeningimmunoglobulin libraries or panels of highly specific binding reagents.Other types of antibodies can be constructed and used therapeutically inmethods of the invention. For example, chimeric antibodies can beconstructed as disclosed in WO 93/03151. Binding proteins which arederived from immunoglobulins and which are multivalent andmultispecific, such as the “diabodies” described in WO 94/13804, alsocan be prepared.

Antibodies according to the invention can be purified by methods wellknown in the art. For example, antibodies can be affinity purified bypassage over a column to which KLK9 is bound. The bound antibodies canthen be eluted from the column using a buffer with a high saltconcentration.

Antisense Oligonucleotides

Antisense oligonucleotides are nucleotide sequences which arecomplementary to a specific DNA or RNA sequence. Once introduced into acell, the complementary nucleotides combine with natural sequencesproduced by the cell to form complexes and block either transcription ortranslation. Preferably, an antisense oligonucleotide is at least 11nucleotides in length, but can be at least 12, 15, 20, 25, 30, 35, 40,45, or 50 or more nucleotides long. Longer sequences also can be used.Antisense oligonucleotide molecules can be provided in a DNA constructand introduced into a cell as described above to decrease the level ofKLK9 gene products in the cell.

Antisense oligonucleotides can be deoxyribonucleotides, ribonucleotides,or a combi-nation of both. Oligonucleotides can be synthesized manuallyor by an automated synthesizer, by covalently linking the 5′ end of onenucleotide with the 3′ end of another nucleotide with non-phosphodiesterintemucleotide linkages such alkyl-phosphonates, phosphorothioates,phosphorodithioates, alkylphosphonothioates, alkylphosphonates,phosphoramidates, phosphate esters, carbamates, acetamidate,carboxymethyl esters, carbonates, and phosphate triesters.

Modifications of KLK9 gene expression can be obtained by designingantisense oligonucleotides which will form duplexes to the control, 5′,or regulatory regions of the KLK9 gene. Oligonucleotides derived fromthe transcription initiation site, e.g., between positions −10 and +10from the start site, are preferred. Similarly, inhibition can beachieved using “triple helix” base-pairing methodology. Triple helixpairing is useful because it causes inhibition of the ability of thedouble helix to open sufficiently for the binding of polymerases,transcription factors, or chaperons.

Therapeutic advances using triplex DNA have been described in theliterature [Nicholls, (1993)]. An antisense oligonucleotide also can bedesigned to block translation of mRNA by preventing the transcript frombinding to ribosomes.

Precise complementarity is not required for successful complex formationbetween an antisense oligonucleotide and the complementary sequence of aKLK9 poly-nucleotide. Antisense oligonucleotides which comprise, forexample, 2, 3, 4, or 5 or more stretches of contiguous nucleotides whichare precisely complementary to a KLK9 polynucleotide, each separated bya stretch of contiguous nucleotides which are not complementary toadjacent KLK9 nucleotides, can provide sufficient targeting specificityfor KLK9 mRNA. Preferably, each stretch of complementary contiguousnucleotides is at least 4, 5, 6, 7, or 8 or more nucleotides in length.Non-complementary intervening sequences are preferably 1, 2, 3, or 4nucleotides in length. One skilled in the art can easily use thecalculated melting point of an antisense-sense pair to determine thedegree of mismatching which will be tolerated between a particularantisense oligonucleotide and a particular KLK9 polynucleotide sequence.Antisense oligonucleotides can be modified without affecting theirability to hybridize to a KLK9 polynucleotide. These modifications canbe internal or at one or both ends of the antisense molecule. Forexample, intemucleoside phosphate linkages can be modified by addingcholesteryl or diamine moieties with varying numbers of carbon residuesbetween the amino groups and terminal ribose. Modified bases and/orsugars, such as arabinose instead of ribose, or a 3′, 5′-substitutedoligonucleotide in which the 3′ hydroxyl group or the 5′ phosphate groupare substituted, also can be employed in a modified antisenseoligonucleotide. These modified oligonucleotides can be prepared bymethods well known in the art.

Ribozymes

Ribozymes are RNA molecules with catalytic activity [Uhlmann, (1987)].Ribozymes can be used to inhibit gene function by cleaving an RNAsequence, as is known in the art. The mechanism of ribozyme actioninvolves sequence-specific hybridization of the ribozyme molecule tocomplementary target RNA, followed by endonucleolytic cleavage. Examplesinclude engineered hammerhead motif ribozyme molecules that canspecifically and efficiently catalyze endonucleolytic cleavage ofspecific nucleotide sequences. The coding sequence of a KLK9polynucleotide can be used to generate ribozymes which will specificallybind to mRNA transcribed from a KLK9 polynucleotide. Methods ofdesigning and constructing ribozymes which can cleave other RNAmolecules in trans in a highly sequence specific manner have beendeveloped and described in the art. For example, the cleavage activityof ribozymes can be targeted to specific RNAs by engineering a discrete“hybridization” region into the ribozyme. The hybridization regioncontains a sequence complementary to the target RNA and thusspecifically hybridizes with the target RNA.

Specific ribozyme cleavage sites within a KLK9 RNA target can beidentified by scanning the target molecule for ribozyme cleavage siteswhich include the following sequences: GUA, GUU, and GUC. Onceidentified, short RNA sequences of between 15 and 20 ribonucleotidescorresponding to the region of the target RNA containing the cleavagesite can be evaluated for secondary structural features which may renderthe target inoperable. Suitability of candidate KLK9 RNA targets alsocan be evaluated by testing accessibility to hybridization withcomplementary oligonucleotides using ribonuclease protection assays. Thenucleotide sequences shown in SEQ ID NO: 1 and its complement providesources of suitable hybridization region sequences. Longer complementarysequences can be used to increase the affinity of the hybridizationsequence for the target. The hybridizing and cleavage regions of theribozyme can be integrally related such that upon hybridizing to thetarget RNA through the complementary regions, the catalytic region ofthe ribozyme can cleave the target.

Ribozymes can be introduced into cells as part of a DNA construct.Mechanical methods, such as microinjection, liposome-mediatedtransfection, electroporation, or calcium phosphate precipitation, canbe used to introduce a ribozyme-containing DNA construct into cells inwhich it is desired to decrease KLK9 expression. Alternatively, if it isdesired that the cells stably retain the DNA construct, the constructcan be supplied on a plasmid and maintained as a separate element orintegrated into the genome of the cells, as is known in the art. Aribozyme-encoding DNA construct can include transcriptional regulatoryelements, such as a promoter element, an enhancer or UAS element, and atranscriptional terminator signal, for controlling transcription ofribozymes in the cells (U.S. Pat. No. 5,641,673). Ribozymes also can beengineered to provide an additional level of regulation, so thatdestruction of mRNA occurs only when both a ribozyme and a target geneare induced in the cells.

Screening/Screening Assays

Regulators

Regulators as used herein, refer to compounds that affect the activityof KLK9 in vivo and/or in vitro. Regulators can be agonists andantagonists of KLK9 polypeptide and can be compounds that exert theireffect on the KLK9 activity via the enzymatic activity, expression,post-translational modifications or by other means. Agonists of KLK9 aremolecules which, when bound to KLK9, increase or prolong the activity ofKLK9. Agonists of KLK9 include proteins, nucleic acids, carbohydrates,small molecules, or any other molecule which activate KLK9. Antagonistsof KLK9 are molecules which, when bound to KLK9, decrease the amount orthe duration of the activity of KLK9. Antagonists include proteins,nucleic acids, carbohydrates, antibodies, small molecules, or any othermolecule which decrease the activity of KLK9.

The term “modulate”, as it appears herein, refers to a change in theactivity of KLK9 polypeptide. For example, modulation may cause anincrease or a decrease in enzymatic activity, binding characteristics,or any other biological, functional, or immunological properties ofKLK9.

As used herein, the terms “specific binding” or “specifically binding”refer to that interaction between a protein or peptide and an agonist,an antibody, or an antagonist. The interaction is dependent upon thepresence of a particular structure of the protein recognized by thebinding molecule (i.e., the antigenic determinant or epitope). Forexample, if an antibody is specific for epitope “A” the presence of apolypeptide containing the epitope A, or the presence of free unlabeledA, in a reaction containing free labeled A and the antibody will reducethe amount of labeled A that binds to the, antibody.

The invention provides methods (also referred to herein as “screeningassays”) for identifying compounds which can be used for the treatmentof diseases related to KLK9. The methods entail the identification ofcandidate or test compounds or agents (e.g., peptides, peptidomimetics,small molecules or other molecules) which bind to KLK9 and/or have astimulatory or inhibitory effect on the biological activity of KLK9 orits expression and then determining which of these compounds have aneffect on symptoms or diseases related to KLK9 in an in vivo assay.

Candidate or test compounds or agents which bind to KLK9 and/or have astimulatory or inhibitory effect on the activity or the expression ofKLK9 are identified either in assays that employ cells which expressKLK9 (cell-based assays) or in assays with isolated KLK9 (cell-freeassays). The various assays can employ a variety of variants of KLK9(e.g., full-length KLK9, a biologically active fragment of KLK9, or afusion protein which includes all or a portion of KLK9). Moreover, KLK9can be derived from any suitable mammalian species (e.g., human KLK9,rat KLK9 or murine KLK9). The assay can be a binding assay entailingdirect or indirect measurement of the binding of a test compound or aknown KLK9 ligand to KLK9. The assay can also be an activity assayentailing direct or indirect measurement of the activity of KLK9. Theassay can also be an expression assay entailing direct or indirectmeasurement of the expression of KLK9 mRNA or KLK9 protein. The variousscreening assays are combined with an in vivo assay entailing measuringthe effect of the test compound on the symptoms of diseases related toKLK9.

The present invention includes biochemical, cell free assays that allowthe identification of inhibitors and agonists of proteases suitable aslead structures for pharmacological drug development. Such assaysinvolve contacting a form of KLK9 (e.g., full-length KLK9, abiologically active fragment of KLK9, or a fusion protein comprising allor a portion of KLK9) with a test compound and determining the abilityof the test compound to act as an antagonist (preferably) or an agonistof the enzymatic activity of KLK9.

The activity of KLK9 molecules of the present invention can be measuredusing a variety of assays that measure KLK9 activity. For example, KLK9enzyme activity can be assessed by a standard in vitro serine/metallo/ .. . protease assay (see, for example, [U.S. Pat. No. 5,057,414]). Thoseof skill in the art are aware of a variety of substrates suitable for invitro assays, such as SucAla-Ala-Pro-Phe-pNA, fluoresceinmono-p-guanidinobenzoate hydrochloride,benzyloxycarbonyl-L-Arginyl-S-benzylester, Nalpha-Benzoyl-L-arginineethyl ester hydrochloride, and the like. In addition, protease assaykits available from commercial sources, such as Calbiochem™ (San Diego,Calif). For general references, see Barrett (Ed.), Methods inEnzymology, Proteolytic Enzymes: Serine and Cysteine Peptidases(Academic Press Inc. 1994), and Barrett et al., (Eds.), Handbook ofProteolytic Enzymes (Academic Press Inc. 1998).

Solution in vitro assays can be used to identify a KLK9 substrate orinhibitor. Solid phase systems can also be used to identify a substrateor inhibitor of a KLK9 polypeptide. For example, a KLK9 polypeptide orKLK9 fusion protein can be immobilized onto the surface of a receptorchip of a commercially available biosensor instrument (BIACORE, BiacoreAB; Uppsala, Sweden). The use of this instrument is disclosed, forexample, by [Karlsson, (1991), and Cunningham and Wells, (1993)].

In brief, a KLK9 polypeptide or fusion protein is covalently attached,using amine or sulfhydryl chemistry, to dextran fibers that are attachedto gold film within a flow cell. A test sample is then passed throughthe cell. If a KLK9 substrate or inhibitor is present in the sample, itwill bind to the immobilized polypeptide or fusion protein, causing achange in the refractive index of the medium, which is detected as achange in surface plasmon resonance of the gold film. This system allowsthe determination on- and off-rates, from which binding affinity can becalculated, and assessment of the stoichiometry of binding, as well asthe kinetic effects of KLK9 mutation. This system can also be used toexamine antibody-antigen interactions, and the interactions of othercomplement/anti-complement pairs.

In one embodiment, the invention provides assays for screening candidateor test compounds which bind to or modulate the activity of KLK9. Suchassays can employ full-length KLK9, a biologically active fragment ofKLK9, or a fusion protein which includes all or a portion of KLK9. Asdescribed in greater detail below, the test compound can be obtained byany suitable means, e.g., from conventional compound libraries.

Determining the ability of the test compound to modulate the activity ofKLK9 can be accomplished, for example, by determining the ability ofKLK9 to bind to or interact with a target molecule. The target moleculecan be a molecule with which KLK9 binds or interacts with in nature. Thetarget molecule can be a component of a signal transduction pathwaywhich facilitates transduction of an extracellular signal. The targetKLK9 molecule can be, for example, a second intracellular protein whichhas catalytic activity or a protein which facilitates the association ofdownstream signaling molecules with KLK9.

Determining the ability of KLK9 to bind to or interact with a targetmolecule can be accomplished by one of the methods described above fordetermining direct binding. In one embodiment, determining the abilityof a polypeptide of the invention to bind to or interact with a targetmolecule can be accomplished by determining the activity of the targetmolecule. For example, the activity of the target molecule can bedetermined by detecting induction of a cellular second messenger of thetarget (e.g., intracellular Ca²⁺, diacylglycerol, IP₃, etc.), detectingcatalytic/enzymatic activity of the target on an appropriate substrate,detecting the induction of a reporter gene (e.g., a regulatory elementthat is responsive to a polypeptide of the invention operably linked toa nucleic acid encoding a detectable marker, e.g., luciferase), ordetecting a cellular response.

In various embodiments of the above assay methods of the presentinvention, it may be desirable to immobilize KLK9 (or a KLK9 targetmolecule) to facilitate separation of complexed from uncomplexed formsof one or both of the proteins, as well as to accommodate automation ofthe assay. Binding of a test compound to KLK9, or interaction of KLK9with a target molecule in the presence and absence of a candidatecompound, can be accomplished in any vessel suitable for containing thereactants. Examples of such vessels include microtitre plates, testtubes, and micro-centrifuge tubes. In one embodiment, a fusion proteincan be provided which adds a domain that allows one or both of theproteins to be bound to a matrix. For example, glutathione-S-transferase(GST) fusion proteins or glutathione-S-transferase fusion proteins canbe adsorbed onto glutathione sepharose beads (Sigma Chemical; St. Louis,Mo.) or glutathione derivatized microtitre plates, which are thencombined with the test compound or the test compound and either thenon-adsorbed target protein or KLK9, and the mixture incubated underconditions conducive to complex formation (e.g., at physiologicalconditions for salt and pH). Following incubation, the beads ormicrotitre plate wells are washed to remove any unbound components andcomplex formation is measured either directly or indirectly, forexample, as described above. Alternatively, the complexes can bedissociated from the matrix, and the level of binding or activity ofKLK9 can be determined using standard techniques.

Other techniques for immobilizing proteins on matrices can also be usedin the screening assays of the invention. For example, either KLK9 orits target molecule can be immobilized utilizing conjugation of biotinand streptavidin. Biotinylated polypeptide of the invention or targetmolecules can be prepared from biotin-NHS (N-hydroxy-succinimide) usingtechniques well known in the art (e.g., biotinylation kit, PierceChemicals; Rockford, Ill.), and immobilized in the wells ofstreptavidin-coated plates (Pierce Chemical). Alternatively, antibodiesreactive with KLK9 or target molecules but which do not interfere withbinding of the polypeptide of the invention to its target molecule canbe derivatized to the wells of the plate, and unbound target orpolypeptide of the invention trapped in the wells by antibodyconjugation. Methods for detecting such complexes, in addition to thosedescribed above for the GST-immobilized complexes, includeimmunodetection of complexes using antibodies reactive with KLK9 ortarget molecule, as well as enzyme-linked assays which rely on detectingan enzymatic activity associated with KLK9 or target molecule.

Another technique for drug screening which may be used provides for highthroughput screening of compounds having suitable binding affinity tothe protein of interest as described in published PCT application WO84/03564. In this method, large numbers of different small testcompounds are synthesized on a solid substrate, such as plastic pins orsome other surface. The test compounds are reacted with KLK9, orfragments thereof, and washed. Bound KLK9 is then detected by methodswell known in the art. Purified KLK9 can also be coated directly ontoplates for use in the aforementioned drug screening techniques.Alternatively, non-neutralizing antibodies can be used to capture thepeptide and immobilize it on a solid support.

In another embodiment, one may use competitive drug screening assays inwhich neutralizing antibodies capable of binding KLK9 specificallycompete with a testcompound for binding KLK9. In this manner, antibodiescan be used to detect the presence of any peptide which shares one ormore antigenic determinants with KLK9.

The screening assay can also involve monitoring the expression of KLK9.For example, regulators of expression of KLK9 can be identified in amethod in which a cell is contacted with a candidate compound and theexpression of KLK9 protein or mRNA in the cell is determined. The levelof expression of KLK9 protein or mRNA the presence of the candidatecompound is compared to the level of expression of KLK9 protein or mRNAin the absence of the candidate compound. The candidate compound canthen be identified as a regulator of expression of KLK9 based on thiscomparison. For example, when expression of KLK9 protein or mRNA proteinis greater (statistically significantly greater) in the presence of thecandidate compound than in its absence, the candidate compound isidentified as a stimulator of KLK9 protein or mRNA expression.Alternatively, when expression of KLK9 protein or mRNA is less(statistically significantly less) in the presence of the candidatecompound than in its absence, the candidate compound is identified as aninhibitor of KLK9 protein or mRNA expression. The level of KLK9 proteinor mRNA expression in the cells can be determined by methods describedbelow.

Binding Assays

For binding assays, the test compound is preferably a small moleculewhich binds to and occupies the active site of KLK9 polypeptide, therebymaking the ligand binding site inaccessible to substrate such thatnormal biological activity is prevented. Examples of such smallmolecules include, but are not limited to, small peptides orpeptide-like molecules. Potential ligands which bind to a polypeptide ofthe invention include, but are not limited to, the natural ligands ofknown KLK9 proteases and analogues or derivatives thereof.

In binding assays, either the test compound or the KLK9 polypeptide cancomprise a detectable label, such as a fluorescent, radioisotopic,chemiluminescent, or enzymatic label, such as horseradish peroxidase,alkaline phosphatase, or luciferase. Detection of a test compound whichis bound to KLK9 polypeptide can then be accomplished, for example, bydirect counting of radioemmission, by scintillation counting, or bydetermining conversion of an appropriate substrate to a detectableproduct. Alternatively, binding of a test compound to a KLK9 polypeptidecan be determined without labeling either of the interactants. Forexample, a microphysiometer can be used to detect binding of a testcompound with a KLK9 polypeptide. A micro-physiometer (e.g.,Cytosensor™) is an analytical instrument that measures the rate at whicha cell acidifies its environment using a light-addressablepotentiometric sensor (LAPS). Changes in this acidification rate can beused as an indicator of the interaction between a test compound and KLK9[Haseloff, (1988)].

Determining the ability of a test compound to bind to KLK9 also can beaccomplished using a technology such as real-time BimolecularInteraction Analysis (BIA) [McConnell, (1992); Sjolander, (1991)]. BIAis a technology for studying biospecific interactions in real time,without labeling any of the interactants (e.g., BIAcore™). Changes inthe optical phenomenon surface plasmon resonance (SPR) can be used as anindication of real-time reactions between biological molecules.

In yet another aspect of the invention, a KLK9-like polypeptide can beused as a “bait protein” in a two-hybrid assay or three-hybrid assay[Szabo, (1995); U.S. Pat. No. 5,283,317), to identify other proteinswhich bind to or interact with KLK9 and modulate its activity.

The two-hybrid system is based on the modular nature of mosttranscription factors, which consist of separable DNA-binding andactivation domains. Briefly, the assay utilizes two different DNAconstructs. For example, in one construct, polynucleotide encoding KLK9can be fused to a polynucleotide encoding the DNA binding domain of aknown transcription factor (e.g., GAL-4). In the other construct a DNAsequence that encodes an unidentified protein (“prey” or “sample”) canbe fused to a polynucleotide that codes for the activation domain of theknown transcription factor. If the “bait” and the “prey” proteins areable to interact in vivo to form an protein-dependent complex, theDNA-binding and activation domains of the transcription factor arebrought into close proximity. This proximity allows transcription of areporter gene (e.g., LacZ), which is operably linked to atranscriptional regulatory site responsive to the transcription factor.Expression of the reporter gene can be detected, and cell coloniescontaining the functional transcription factor can be isolated and usedto obtain the DNA sequence encoding the protein which interacts withKLK9.

It may be desirable to immobilize either the KLK9 (or polynucleotide) orthe test compound to facilitate separation of the bound form fromunbound forms of one or both of the interactants, as well as toaccommodate automation of the assay. Thus, either the KLK9-likepolypeptide (or polynucleotide) or the test compound can be bound to asolid support. Suitable solid supports include, but are not limited to,glass or plastic slides, tissue culture plates, microtiter wells, tubes,silicon chips, or particles such as beads (including, but not limitedto, latex, polystyrene, or glass beads). Any method known in the art canbe used to attach KLK9-like polypeptide (or polynucleotide) or testcompound to a solid support, including use of covalent and non-covalentlinkages, passive absorption, or pairs of binding moieties attachedrespectively to the polypeptide (or polynucleotide) or test compound andthe solid support. Test compounds are preferably bound to the solidsupport in an array, so that the location of individual test compoundscan be tracked. Binding of a test compound to KLK9 (or a polynucleotideencoding for KLK9) can be accomplished in any vessel suitable forcontaining the reactants. Examples of such vessels include microtiterplates, test tubes, and microcentrifuge tubes.

In one embodiment, KLK9 is a fusion protein comprising a domain thatallows binding of KLK9 to a solid support. For example,glutathione-S-transferase fusion proteins can be adsorbed ontoglutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) orglutathione derivatized microtiter plates, which are then combined withthe test compound or the test compound and the non-adsorbed KLK9; themixture is then incubated under conditions conducive to complexformation (e.g., at physiological conditions for salt and pH). Followingincubation, the beads or microtiter plate wells are washed to remove anyunbound components. Binding of the interactants can be determined eitherdirectly or indirectly, as described above. Alternatively, the complexescan be dissociated from the solid support before binding is determined.

Other techniques for immobilizing proteins or polynucleotides on a solidsupport also can be used in the screening assays of the invention. Forexample, either KLK9 (or a polynucleotide encoding KLK9) or a testcompound can be immobilized utilizing conjugation of biotin andstreptavidin. Biotinylated KLK9 (or a polynucleotide encodingbiotinylated KLK9) or test compounds can be prepared from biotin-NHS(N-hydroxysuccinimide) using techniques well known in the art (e.g.,biotinylation kit, Pierce Chemicals, Rockford, Ill.) and immobilized inthe wells of streptavidin-coated plates (Pierce Chemical).Alternatively, antibodies which specifically bind to KLK9,polynucleotide, or a test compound, but which do not interfere with adesired binding site, such as the active site of KLK9, can bederivatized to the wells of the plate. Unbound target or protein can betrapped in the wells by antibody conjugation.

Methods for detecting such complexes, in addition to those describedabove for the GST-immobilized complexes, include immunodetection ofcomplexes using antibodies which specifically bind to KLK9 polypeptideor test compound, enzyme-linked assays which rely on detecting anactivity of KLK9 polypeptide, and SDS gel electrophoresis undernon-reducing conditions.

Screening for test compounds which bind to a KLK9 polypeptide orpolynucleotide also can be carried out in an intact cell. Any cell whichcomprises a KLK9 polypeptide or polynucleotide can be used in acell-based assay system. A KLK9 polynucleotide can be naturallyoccurring in the cell or can be introduced using techniques such asthose described above. Binding of the test compound to KLK9 or apolynucleotide encoding KLK9 is determined as described above.

Functional Assays

Test compounds can be tested for the ability to increase or decreaseKLK9 activity of a KLK9 polypeptide. The KLK9 activity can be measured,for example, using methods described in the specific examples, below.KLK9 activity can be measured after contacting either a purified KLK9 oran intact cell with a test compound. A test compound which decreasesKLK9 activity by at least about 10, preferably about 50, more preferablyabout 75, 90, or 100% is identified as a potential agent for decreasingKLK9 activity. A test compound which increases KLK9 activity by at leastabout 10, preferably about S0, more preferably about 75, 90, or 100% isidentified as a potential agent for increasing KLK9 activity.

Gene Expression

In another embodiment, test compounds which increase or decrease KLK9gene expression are identified. As used herein, the term “correlateswith expression of a polynucleotide” indicates that the detection of thepresence of nucleic acids, the same or related to a nucleic acidsequence encoding KLK9, by northern analysis or realtime PCR isindicative of the presence of nucleic acids encoding KLK9 in a sample,and thereby correlates with expression of the transcript from thepolynucleotide encoding KLK9. The term “microarray”, as used herein,refers to an array of distinct polynucleotides or oligonucleotidesarrayed on a substrate, such as paper, nylon or any other type ofmembrane, filter, chip, glass slide, or any other suitable solidsupport. A KLK9 polynucleotide is contacted with a test compound, andthe expression of an RNA or polypeptide product of KLK9 polynucleotideis determined. The level of expression of appropriate mRNA orpolypeptide in the presence of the test compound is compared to thelevel of expression of mRNA or polypeptide in the absence of the testcompound. The test compound can then be identified as a regulator ofexpression based on this comparison. For example, when expression ofmRNA or polypeptide is greater in the presence of the test compound thanin its absence, the test compound is identified as a stimulator orenhancer of the mRNA or polypeptide expression. Alternatively, whenexpression of the mRNA or polypeptide is less in the presence of thetest compound than in its absence, the test compound is identified as aninhibitor of the mRNA or polypeptide expression.

The level of KLK9 mRNA or polypeptide expression in the cells can bedetermined by methods well known in the art for detecting mRNA orpolypeptide. Either qualitative or quantitative methods can be used. Thepresence of polypeptide products of KLK9 polynucleotide can bedetermined, for example, using a variety of techniques known in the art,including immunochemical methods such as radioimmunoassay, Westernblotting, and immunohistochemistry. Alternatively, polypeptide synthesiscan be determined in vivo, in a cell culture, or in an in vitrotranslation system by detecting incorporation of labelled amino acidsinto KLK9.

Such screening can be carried out either in a cell-free assay system orin an intact cell. Any cell which expresses KLK9 polynucleotide can beused in a cell-based assay system. The KLK9 polynucleotide can benaturally occurring in the cell or can be introduced using techniquessuch as those described above. Either a primary culture or anestablished cell line can be used.

Test Compounds

Suitable test compounds for use in the screening assays of the inventioncan be obtained from any suitable source, e.g., conventional compoundlibraries. The test compounds can also be obtained using any of thenumerous approaches in combinatorial library methods known in the art,including: biological libraries; spatially addressable parallel solidphase or solution phase libraries; synthetic library methods requiringdeconvolution; the “one-bead one-compound” library method; and syntheticlibrary methods using affinity chromatography selection. The biologicallibrary approach is limited to peptide libraries, while the other fourapproaches are applicable to peptide, non-peptide oligomer or smallmolecule libraries of compounds [Lam, (1997)]. Examples of methods forthe synthesis of molecular libraries can be found in the art. Librariesof compounds may be presented in solution or on beads, bacteria, spores,plasmids or phage.

Modeling of Regulators

Computer modeling and searching technologies permit identification ofcompounds, or the improvement of already identified compounds, that canmodulate KLK9 expression or activity. Having identified such a compoundor composition, the active sites or regions are identified. Such sitesmight typically be the enzymatic active site, regulator binding sites,or ligand binding sites. The active site can be identified using methodsknown in the art including, for example, from the amino acid sequencesof peptides, from the nucleotide sequences of nucleic acids, or fromstudy of complexes of the relevant compound or composition with itsnatural ligand. In the latter case, chemical or X-ray crystallographicmethods can be used to find the active site by finding where on thefactor the complexed ligand is found.

Next, the three dimensional geometric structure of the active site isdetermined. This can be done by known methods, including X-raycrystallography, which can determine a complete molecular structure. Onthe other hand, solid or liquid phase NMR can be used to determinecertain intramolecular distances. Any other experimental method ofstructure determination can be used to obtain partial or completegeometric structures. The geometric structures may be measured with acomplexed ligand, natural or artificial, which may increase the accuracyof the active site structure determined.

If an incomplete or insufficiently accurate structure is determined, themethods of computer based numerical modeling can be used to complete thestructure or improve its accuracy. Any recognized modeling method may beused, including parameterized models specific to particular biopolymerssuch as proteins or nucleic acids, molecular dynamics models based oncomputing molecular motions, statistical mechanics models based onthermal ensembles, or combined models. For most types of models,standard molecular force fields, representing the forces betweenconstituent atoms and groups, are necessary, and can be selected fromforce fields known in physical chemistry. The incomplete or lessaccurate experimental structures can serve as constraints on thecomplete and more accurate structures computed by these modelingmethods.

Finally, having determined the structure of the active site, eitherexperimentally, by modeling, or by a combination, candidate modulatingcompounds can be identified by searching databases containing compoundsalong with information on their molecular structure. Such a search seekscompounds having structures that match the determined active sitestructure and that interact with the groups defining the active site.Such a search can be manual, but is preferably computer assisted. Thesecompounds found from this search are potential KLK9 modulatingcompounds.

Alternatively, these methods can be used to identify improved modulatingcompounds from an already known modulating compound or ligand. Thecomposition of the known compound can be modified and the structuraleffects of modification can be determined using the experimental andcomputer modeling methods described above applied to the newcomposition. The altered structure is then compared to the active sitestructure of the compound to determine if an improved fit or interactionresults. In this manner systematic variations in composition, such as byvarying side groups, can be quickly evaluated to obtain modifiedmodulating compounds or ligands of improved specificity or activity.

Therapeutic Indications and Methods

It was found by the present applicant that KLK9 is expressed in varioushuman tissues.

Neurology

CNS disorders include disorders of the central nervous system as well asdisorders of the peripheral nervous system.

CNS disorders include, but are not limited to brain injuries,cerebrovascular diseases and their consequences, Parkinson's disease,corticobasal degeneration, motor neuron disease, dementia, includingALS, multiple sclerosis, traumatic brain injury, stroke, post-stroke,post-traumatic brain injury, and small-vessel cerebrovascular disease.Dementias, such as Alzheimer's disease, vascular dementia, dementia withLewy bodies, frontotemporal dementia and Parkinsonism linked tochromosome 17, frontotemporal dementias, including Pick's disease,progressive nuclear palsy, corticobasal degeneration, Huntington'sdisease, thalamic degeneration, Creutzfeld-Jakob dementia, HIV dementia,schizophrenia with dementia, and Korsakoff's psychosis, within themeaning of the definition are also considered to be CNS disorders.

Similarly, cognitive-related disorders, such as mild cognitiveimpairment, age-associated memory impairment, age-related cognitivedecline, vascular cognitive impairment, attention deficit disorders,attention deficit hyperactivity disorders, and memory disturbances inchildren with learning disabilities are also considered to be CNSdisorders.

Pain, within the meaning of this definition, is also considered to be aCNS disorder. Pain can be associated with CNS disorders, such asmultiple sclerosis, spinal cord injury, sciatica, failed back surgerysyndrome, traumatic brain injury, epilepsy, Parkinson's disease,post-stroke, and vascular lesions in the brain and spinal cord (e.g.,infarct, hemorrhage, vascular malformation). Non-central neuropathicpain includes that associated with post mastectomy pain, phantomfeeling, reflex sympathetic dystrophy (RSD), trigeminalneuralgiaradioculopathy, post-surgical pain, HIV/AIDS related pain,cancer pain, metabolic neuropathies (e.g., diabetic neuropathy,vasculitic neuropathy secondary to connective tissue disease),paraneoplastic polyneuropathy associated, for example, with carcinoma oflung, or leukemia, or lymphoma, or carcinoma of prostate, colon orstomach, trigeminal neuralgia, cranial neuralgias, and post-herpeticneuralgia. Pain associated with peripheral nerve damage, central pain(i.e. due to cerebral ischemia) and various chronic pain i.e., lumbago,back pain (low back pain), inflammatory and/or rheumatic pain. Headachepain (for example, migraine with aura, migraine without aura, and othermigraine disorders), episodic and chronic tension-type headache,tension-type like headache, cluster headache, and chronic paroxysmalhemicrania are also CNS disorders.

Visceral pain such as pancreatits, intestinal cystitis, dysmenorrhea,irritable Bowel syndrome, Crohn's disease, biliary colic, ureteralcolic, myocardial infarction and pain syndromes of the pelvic cavity,e.g., vulvodynia, orchialgia, urethral syndrome and protatodynia arealso CNS disorders.

Also considered to be a disorder of the nervous system are acute pain,for example postoperative pain, and pain after trauma.

The human KLK9 is highly expressed in the following brain tissues:cerebellum (left), cerebral meninges, dorsal root ganglia, retina. Theexpression in brain tissues demonstrates that the human KLK9 or mRNA canbe utilized to diagnose nervous system diseases. Additionally theactivity of the human KLK9 can be modulated to treat nervous systemdiseases.

Cardiovascular Disorders

Heart failure is defined as a pathophysiological state in which anabnormality of cardiac function is responsible for the failure of theheart to pump blood at a rate commensurate with the requirement of themetabolizing tissue. It includes all forms of pumping failures such ashigh-output and low-output, acute and chronic, right-sided orleft-sided, systolic or diastolic, independent of the underlying cause.

Myocardial infarction (MI) is generally caused by an abrupt decrease incoronary blood flow that follows a thrombotic occlusion of a coronaryartery previously narrowed by arteriosclerosis. MI prophylaxis (primaryand secondary prevention) is included as well as the acute treatment ofMI and the prevention of complications.

Ischemic diseases are conditions in which the coronary flow isrestricted resulting in a perfusion which is inadequate to meet themyocardial requirement for oxygen. This group of diseases includesstable angina, unstable angina and asymptomatic ischemia.

Arrhythmias include all forms of atrial and ventriculartachyarrhythmias, atrial tachycardia, atrial flutter, atrialfibrillation, atrio-ventricular reentrant tachycardia, preexitationsyndrome, ventricular tachycardia, ventricular flutter, ventricularfibrillation, as well as bradycardic forms of arrhythmias.

Hypertensive vascular diseases include primary as well as all kinds ofsecondary arterial hypertension, renal, endocrine, neurogenic, others.The genes may be used as drug targets for the treatment of hypertensionas well as for the prevention of all complications arising fromcardiovascular diseases.

Peripheral vascular diseases are defined as vascular diseases in whicharterial and/or venous flow is reduced resulting in an imbalance betweenblood supply and tissue oxygen demand. It includes chronic peripheralarterial occlusive disease (PAOD), acute arterial thrombosis andembolism, inflammatory vascular disorders, Raynaud's phenomenon andvenous disorders.

Atherosclerosis is a cardiovascular disease in which the vessel wall isremodeled, compromising the lumen of the vessel. The atheroscleroticremodeling process involves accumulation of cells, both smooth musclecells and monocyte/macrophage inflammatory cells, in the intima of thevessel wall. These cells take up lipid, likely from the circulation, toform a mature atherosclerotic lesion. Although the formation of theselesions is a chronic process, occurring over decades of an adult humanlife, the majority of the morbidity associated with atherosclerosisoccurs when a lesion ruptures, releasing thrombogenic debris thatrapidly occludes the artery. When such an acute event occurs in thecoronary artery, myocardial infarction can ensue, and in the worst case,can result in death.

The formation of the atherosclerotic lesion can be considered to occurin five overlapping stages such as migration, lipid accumulation,recruitment of inflammatory cells, proliferation of vascular smoothmuscle cells, and extracellular matrix deposition. Each of theseprocesses can be shown to occur in man and in animal models ofatherosclerosis, but the relative contribution of each to the pathologyand clinical significance of the lesion is unclear.

Thus, a need exists for therapeutic methods and agents to treatcardiovascular pathologies, such as atherosclerosis and other conditionsrelated to coronary artery disease.

Cardiovascular diseases include but are not limited to disorders of theheart and the vascular system like congestive heart failure, myocardialinfarction, ischemic diseases of the heart, all kinds of atrial andventricular arrhythmias, hypertensive vascular diseases, peripheralvascular diseases, and atherosclerosis.

Too high or too low levels of fats in the bloodstream, especiallycholesterol, can cause long-term problems. The risk to developatherosclerosis and coronary artery or carotid artery disease (and thusthe risk of having a heart attack or stroke) increases with the totalcholesterol level increasing. Nevertheless, extremely low cholesterollevels may not be healthy. Examples of disorders of lipid metabolism arehyperlipidemia (abnormally high levels of fats (cholesterol,triglycerides, or both) in the blood, may be caused by family history ofhyperlipidemia), obesity, a high-fat diet, lack of exercise, moderate tohigh alcohol consumption, cigarette smoking, poorly controlled diabetes,and an underactive thyroid gland), hereditary hyperlipidemias (type Ihyperlipoproteinemia (familial hyperchylomicronemia), type IIhyperlipoproteinemia (familial hypercholesterolemia), type IIIhyperlipoproteinemia, type IV hyperlipoproteinemia, or type Vhyperlipoproteinemia), hypolipoproteinemia, lipidoses (caused byabnormalities in the enzymes that metabolize fats), Gaucher's disease,Niemann-Pick disease, Fabry's disease, Wolman's disease,cerebrotendinous xanthomatosis, sitosterolemia, Refsum's disease, orTay-Sachs disease.

Kidney disorders may lead to hypertension or hypotension. Examples forkidney problems possibly leading to hypertension are renal arterystenosis, pyelonephritis, glomerulonephritis, kidney tumors, polycistickidney disease, injury to the kidney, or radiation therapy affecting thekidney. Excessive urination may lead to hypotension.

The human KLK9 is highly expressed in the following cardiovascularrelated tissues: heart ventricle (left), aorta, artery and vein.Expression in the above mentioned tissues demonstrates that the humanKLK9 or mRNA can be utilized to diagnose of cardiovascular diseases.Additionally the activity of the human KLK9 can be modulated to treatcardiovascular diseases.

Hematological Disorders

Hematological disorders comprise diseases of the blood and all itsconstituents as well as diseases of organs and tissues involved in thegeneration or degradation of all the constituents of the blood. Theyinclude but are not limited to 1) Anemias, 2) MyeloproliferativeDisorders, 3) Hemorrhagic Disorders, 4) Leukopenia, 5) EosinophilicDisorders, 6) Leukemias, 7) Lymphomas, 8) Plasma Cell Dyscrasias, 9)Disorders of the Spleen in the course of hematological disorders.Disorders according to 1) include, but are not limited to anemias due todefective or deficient hem synthesis, deficient erythropoiesis.Disorders according to 2) include, but are not limited to polycythemiavera, tumor-associated erythrocytosis, myelofibrosis, thrombocythemia.Disorders according to 3) include, but are not limited to vasculitis,thrombocytopenia, heparin-induced thrombocytopenia, thromboticthrombocytopenic purpura, hemolytic-uremic syndrome, hereditary andacquired disorders of platelet function, hereditary coagulationdisorders. Disorders according to 4) include, but are not limited toneutropenia, lymphocytopenia. Disorders according to 5) include, but arenot limited to hypereosinophilia, idiopathic hypereosinophilic syndrome.Disorders according to 6) include, but are not limited to acute myeloicleukemia, acute lymphoblastic leukemia, chronic myelocytic leukemia,chronic lymphocytic leukemia, myelodysplastic syndrome. Disordersaccording to 7) include, but are not limited to Hodgkin's disease,non-Hodgkin's lymphoma, Burkitt's lymphoma, mycosis fungoides cutaneousT-cell lymphoma. Disorders according to 8) include, but are not limitedto multiple myeloma, macroglobulinemia, heavy chain diseases.

In extension of the preceding idiopathic thrombocytopenic purpura, irondeficiency anemia, megaloblastic anemia (vitamin B 12 deficiency),aplastic anemia, thalassemia, malignant lymphoma bone marrow invasion,malignant lymphoma skin invasion, hemolytic uremic syndrome, giantplatelet disease are considered to be hematological diseases too.

The human KLK9 is highly expressed in the following tissues of thehematological system: lymphnode, thrombocytes. The expression in theabove mentioned tissues demonstrates that the human KLK9 or mRNA can beutilized to diagnose of hematological diseases. Additionally theactivity of the human KLK9 can be modulated to treat hematologicaldisorders.

Gastrointestinal and Liver Diseases

Gastrointestinal diseases comprise primary or secondary, acute orchronic diseases of the organs of the gastrointestinal tract which maybe acquired or inherited, benign or malignant or metaplastic, and whichmay affect the organs of the gastrointestinal tract or the body as awhole. They comprise but are not limited to 1) disorders of theesophagus like achalasia, vigoruos achalasia, dysphagia, cricopharyngealincoordination, pre-esophageal dysphagia, diffuse esophageal spasm,globus sensation, Barrett's metaplasia, gastroesophageal reflux, 2)disorders of the stomach and duodenum like functional dyspepsia,inflammation of the gastric mucosa, gastritis, stress gastritis, chronicerosive gastritis, atrophy of gastric glands, metaplasia of gastrictissues, gastric ulcers, duodenal ulcers, neoplasms of the stomach, 3)disorders of the pancreas like acute or chronic pancreatitis,insufficiency of the exocrinic or endocrinic tissues of the pancreaslike steatorrhea, diabetes, neoplasms of the exocrine or endocrinepancreas like 3.1) multiple endocrine neoplasia syndrome, ductaladenocarcinoma, cystadenocarcinoma, islet cell tumors, insulinoma,gastrinoma, carcinoid tumors, glucagonoma, Zollinger-Ellison syndrome,Vipoma syndrome, malabsorption syndrome, 4) disorders of the bowel likechronic inflammatory diseases of the bowel, Crohn's disease, ileus,diarrhea and constipation, colonic inertia, megacolon, malabsorptionsyndrome, ulcerative colitis, 4.1) functional bowel disorders likeirritable bowel syndrome, 4.2) neoplasms of the bowel like familialpolyposis, adenocarcinoma, primary malignant lymphoma, carcinoid tumors,Kaposi's sarcoma, polyps, cancer of the colon and rectum.

Liver diseases comprise primary or secondary, acute or chronic diseasesor injury of the liver which may be acquired or inherited, benign ormalignant, and which may affect the liver or the body as a whole. Theycomprise but are not limited to disorders of the bilirubin metabolism,jaundice, syndroms of Gilbert's, Crigler-Najjar, Dubin-Johnson andRotor; intrahepatic cholestasis, hepatomegaly, portal hypertension,ascites, Budd-Chiari syndrome, portal-systemic encephalopathy, fattyliver, steatosis, Reye's syndrome, liver diseases due to alcohol,alcoholic hepatitis or cirrhosis, fibrosis and cirrhosis, fibrosis andcirrhosis of the liver due to inborn errors of metabolism or exogenoussubstances, storage diseases, syndromes of Gaucher's, Zellweger's,Wilson's disease, acute or chronic hepatitis, viral hepatitis and itsvariants, inflammatory conditions of the liver due to viruses, bacteria,fungi, protozoa, helminths; drug induced disorders of the liver, chronicliver diseases like primary sclerosing cholangitis,alpha₁,-antitrypsin-deficiency, primary biliary cirrhosis, postoperativeliver disorders like postoperative intrahepatic cholestasis, hepaticgranulomas, vascular liver disorders associated with systemic disease,benign or malignant neoplasms of the liver, disturbance of livermetabolism in the new-born or prematurely born.

The human KLK9 is highly expressed in the following tissues of thegastroenterological system: esophagus, ileum chronic inflammation,rectum, liver liver cirrhosis. The expression in the above mentionedtissues and in particular the differential expression between diseasedtissue ileum chronic inflammation and healthy tissue ileum, betweendiseased tissue liver liver cirrhosis and healthy tissue liverdemonstrates that the human KLK9 or mRNA can be utilized to diagnose ofgastroenterological disorders. Additionally the activity of the humanKLK9 can be modulated to treat gastroenterological disorders.

Dermatologic Disorders

The skin serves several functions. It's an multi-layered organ systemthat builds an effective protective cover and regulates bodytemperature, senses painful and pleasant stimuli, keeps substances fromentering the body, and provides a shield from the sun's harmful effects.Skin color, texture, and folds help mark people as individuals. Thus,skin disorders or diseases often have important consequences forphysical and mental health. Skin disorders include, but are not limitedto the conditions described in the following.

Itching (pruritus) is a sensation that instinctively demands scratching,which may be caused by a skin condition or a systemic diseas.

Superficial Skin Disorders affect the uppermost layer of the skin, thestratum corneum or the keratin layer, and it consists of many layers offlattened, dead cells and acts as a barrier to protect the underlyingtissue from injury and infection. Disorders of the superficial skinlayers involve the stratum corneum and deeper layers of the epidermis.

Examples of superficial skin disorders are provided in the following.

Dry skin often occurs in people past middle age, severe dry skin(ichthyosis) results from an inherited scaling disease, such asichthyosis vulgaris or epidermolytic hyperkeratosis. Ichthyosis alsoresults from nonhereditary disorders, such as leprosy, underactivethyroid, lymphoma, AIDS, and sarcoidosis.

Keratosis pilaris is a common disorder in which dead cells shed from theupper layer of skin and form plugs that fill the openings of hairfollicles.

A callus is an area on the stratum corneum or keratin layer, thatbecomes abnormally thick in response to repeated rubbing.

A corn is a pea-sized, thickened area of keratin that occurs on thefeet.

Psoriasis is a chronic, recurring disease recognizable by silveryscaling bumps and various-sized plaques (raised patches). An abnormallyhigh rate of growth and turnover of skin cells causes the scaling.Pityriasis rosea is a mild disease that causes scaly, rose-colored,inflamed skin. Pityriasis rosea is possibly caused by an infectiousagent, although none has been identified.

Lichen planus, a recurring itchy disease, starts as a rash of smalldiscrete bumps that then combine and become rough, scaly plaques (raisedpatches).

Dermatitis (eczema) is an inflammation of the upper layers of the skin,causing blisters, redness, swelling, oozing, scabbing, scaling, andusually itching.

Forms of dermatitis are contact dermatitis, or chronic dermatitis of thehands and feet, e.g. Pompholyx.

Further examples of dermatitic disorders are atopic dermatitis,seborrheic dermatitis, nummular dermatitis, generalized exfoliativedermatitis, stasis dermatitis, or localized scratch dermatitis (lichensimplex chronicus, neurodermatitis).

Other skin disorders are caused by inflammation. The skin can break outin a variety of rashes, sores, and blisters. Some skin eruptions caneven be life threatening.

Drug rashes are side effects of medications, mainly allergic reactionsto medications. Toxic epidermal necrolysis is a life-threatening skindisease in which the top layer of the skin peels off in sheets. Thiscondition can be caused by a reaction to a drug, or by some otherserious disease.

Erythema multiforme, often caused by herpes simplex is a disordercharacterized by patches of red, raised skin that often look liketargets and usually are distributed symmetrically over the body.

Erythema nodosum is an inflammatory disorder that produces tender redbumps (nodules) under the skin, most often over the shins butoccasionally on the arms and other areas.

Granuloma annulare is a chronic skin condition of unknown cause in whichsmall, firm, raised bumps form a ring with normal or slightly sunkenskin in the center.

Some skin disorders are characterized as blistering diseases. Threeautoimmune diseases—pemphigus, bullous pemphigoid, and dermatitisherpetiformis—are among the most serious.

Pemphigus is an uncommon, sometimes fatal, disease in which blisters(bullae) of varying sizes break out on the skin, the lining of themouth, and other mucous membranes.

Bullous pemphigoid is an autoimmune disease that causes blistering.

Dermatitis herpetiformis is an autoimmune disease in which clusters ofintensely itchy, small blisters and hive-like swellings break out andpersist. In people with the disease, proteins in wheat, rye, barley, andoat products activate the immune system, which attacks parts of the skinand somehow causes the rash and itching.

Sweating disorders also belong to skin disorders.

Prickly heat is an itchy skin rash caused by trapped sweat.

Excessive sweating hyperhidrosis) may affect the entire surface of theskin, but often it's limited to the palms, soles, armpits, or groin. Theaffected area is often pink or bluish white, and in severe cases theskin may be cracked, scaly, and soft, especially on the feet.

Skin disorders can affect the sebaceous glands. The sebaceous glands,which secrete oil onto the skin, lie in the dermis, the skin layer justbelow the surface layer (epidermis). Sebaceous gland disorders includeacne, rosacea, perioral dermatitis, and sebaceous cysts.

Acne is a common skin condition in which the skin pores become clogged,leading to pimples and inflamed, infected abscesses (collections ofpus). Acne tends to develop in teenagers.

Acne is further subdivided in superficial acne or deep acne.

Rosacea is a persistent skin disorder that produces redness, tinypimples, and broken blood vessels, usually on the central area of theface.

Perioral dermatitis is a red, often bumpy rash around the mouth and onthe chin.

A sebaceous cyst (keratinous cyst) is a slow-growing bump containingdead skin, skin excretions, and other skin particles. These cysts may besmall and can appear anywhere.

Hair Disorders also are skin disorders. Hair disorders include excessivehairiness, baldness, and ingrown beard hairs.

The skin can be infected by bacteria. Bacterial skin infections canrange in seriousness from minor acne to a life-threatening condition,such as staphylococcal scalded skin syndrome. The most common bacterialskin infections are caused by Staphylococcus and Streptococcus. Riskfactors for skin infections are for example diabetes, AIDS or skinleasons.

Inpetigo is a skin infection, caused by Staphylococcus or Streptococcus,leading to the formation of small pus-filled blisters (pustules).

Folliculitis is an inflammation of the hair follicles caused byinfection with Staphylococcus. The infection damages the hairs, whichcan be easily pulled out.

Boils (furuncles) are large, tender, swollen, raised areas caused bystaphylococcal infection around hair follicles.

Carbuncles are clusters of boils that result in extensive sloughing ofskin and scar formation. Carbuncles develop and heal more slowly thansingle boils and may lead to fever and fatigue.

Erysipelas is a skin infection caused by Streptococcus. A shiny, red,slightly swollen, tender rash develops, often with small blisters. Lymphnodes around the infected area may become enlarged and painful.

Cellulitis is a spreading infection in, and sometimes beneath, the deeplayers of the skin. Cellulitis most often results from a streptococcalinfection or a staphylococcal infection. However, many other bacteriacan also cause cellulitis.

Paronychia is an infection around the edge of a fingernail or toenail.Paronychia can be caused by many different bacteria, includingPseudomonas and Proteus, and by fungi, such as Candida.

Staphylococcal scalded skin syndrome is a widespread skin infection thatcan lead to toxic shock syndrome, in which the skin peels off as thoughburned. Certain types of staphylococci produce a toxic substance thatcauses the top layer of skin (epidermis) to split from the rest of theskin.

Erythrasma is an infection of the top layers of the skin by thebacterium Corynebacterium minutissimum.

Skin infections are often caused by fungi. Fungi that infect the skin(dermatophytes) live only in the dead, topmost layer (stratum corneum)and don't penetrate deeper. Some fungal infections cause no symptoms orproduce only a small amount of irritation, scaling, and redness. Otherfungal infections cause itching, swelling, blisters, and severe scaling.

Ringworm is a fungal skin infection caused by several different fungiand generally classified by its location on the body.

Examples are Athlete's foot (foot ringworm, caused by eitherTrichophyton or Epidermophyton), jock itch (groin ringworm, can becaused by a variety of fungi and yeasts), scalp ringworm, caused byTrichophyton or Microsporum), nail ringworm and body ringworm (caused byTrichophyton).

Candidiasis (yeast infection, moniliasis) is an infection by the yeastCandida. Candida usually infects the skin and mucous membranes, such asthe lining of the mouth and vagina. Rarely, it invades deeper tissues aswell as the blood, causing life-threatening systemic candidiasis. Thefollowing types of candida infections can be distinguished: Infectionsin skinfolds (intertriginous infections), vaginal and penile candidainfections (vulvovaginitis), thrush, Perlèche (candida infection at thecorners of the mouth), candidal paronychia (candida growing in the nailbeds, produces painful swelling and pus).

Tinea versicolor is a fungal infection that causes white to light brownpatches on the skin.

The skin can also be affected by parasites, mainly tiny insects orworms.

Scabies is a mite infestation that produces tiny reddish pimples andsevere itching. Scabies is caused by the itch mite Sarcoptes scabiei.

Lice infestation (pediculosis) causes intense itching and can affectalmost any area of the skin. Head lice and pubic lice are two differentspecies.

Creeping eruption (cutaneous larva migrans) is a hookworm infectiontransmitted from warm, moist soil to exposed skin. The infection iscaused by a hookworm that normally inhabits dogs and cats.

Many types of viruses invade the skin. The medically important oncecause warts and cold sores (fever blisters) on the lip. Warts are causedby the papillomavirus, and cold sores are caused by the herpes simplexvirus. Another important group of viruses that infect the skin belongsto the poxvirus family. Chickenpox remains a common childhood infection.A poxvirus also causes molluscum contagiosum, which is an infection ofthe skin by a poxvirus that causes skin-colored, smooth, waxy bumps.

Sunlight can cause severe skin damage. Sunburn results from anoverexposure to ultraviolet B (UVB) rays. Some sunburned people developa fever, chills, and weakness, and those with very bad sunburns even maygo into shock—low blood pressure, and fainting.

People who are in the sun a lot have an increased risk of skin cancers,including squamous cell carcinoma, basal cell carcinoma, and to somedegree, malignant melanoma.

Drugs, among other causes, can cause skin photosensitivity reactionswhich can occur after only a few minutes of sun exposure. Thesereactions include redness, peeling, hives, blisters, and thickened,scaling patches (photosensitivity).

Some skin disorders are characterized as Pigment Disorders.

Albinism is a rare, inherited disorder in which no melanin is formed.

Vitiligo is a condition in which a loss of melanocytes results insmooth, whitish patches of skin, which may occur after unusual physicaltrauma and tends to occur with certain other diseases, includingAddison's disease, diabetes, pernicious anemia, and thyroid disease.

Tinea versicolor is a fungal infection of the skin that sometimesresults in hyperpigmentation.

Melasma appears on the face (usually the forehead, cheeks, temples, andjaws) as a roughly symmetric group of dark brown patches of pigmentationthat are often clearly delineated.

Skin growths, which are abnormal accumulations of different types ofcells, may be present at birth or develop later. Noncancerous (benign)growth and cancerous (malignant) growth types are distinguished.

Moles (nevi) are small, usually dark, skin growths that develop frompigment-producing cells in the skin (melanocytes). Most moles areharmless. However, noncancerous moles can develop into malignantmelanoma.

Skin tags are soft, small, flesh-colored or slightly darker skin flapsthat appear mostly on the neck, in the armpits, or in the groin.

Lipomas are soft deposits of fatty material that grow under the skin,causing round or oval lumps.

Angiomas are collections of abnormally dense blood or lymph vessels thatare usually located in and below the skin and that cause red or purplediscolorations.

Examples of angiomas are port-wine stains, strawberry marks, cavernoushemangiomas, spider angiomas, and lymphangiomas.

Pyogenic granulomas are scarlet, brown, or blue-black slightly raisedareas caused by increased growth of capillaries (the smallest bloodvessels) and swelling of the surrounding tissue.

Seborrheic keratoses (sometimes called seborrheic warts) areflesh-colored, brown, or black growths that can appear anywhere on theskin.

Dermatofibromas are small, red-to-brown bumps (nodules) that result froman accumulation of fibroblasts, the cells that populate the soft tissueunder the skin.

Keratoacanthomas are round, firm, usually flesh-colored growths thathave an unusual central crater containing a pasty material.

Keloids are smooth, shiny, slightly pink, often dome-shaped,proliferative growths of fibrous tissue that form over areas of injuryor over surgical wounds.

Skin cancer is the most common form of cancer, but most types of skincancers are curable.

Basal cell carcinoma is a cancer that originates in the lowest layer ofthe epidermis.

Squamous cell carcinoma is cancer that originates in the middle layer ofthe epidermis.

Bowen's disease is a form of squamous cell carcinoma that's confined tothe epidermis and hasn't yet invaded the underlying dermis.

Melanoma is a cancer that originates in the pigment-producing cells ofthe skin (melanocytes).

Kaposi's sarcoma is a cancer that originates in the blood vessels,usually of the skin.

Paget's disease is a rare type of skin cancer that looks like aninflamed, reddened patch of skin (dermatitis); it originates in glandsin or under the skin.

The human KLK9 is highly expressed in the following dermatologicaltissues: skin. The expression in liver tissues demonstrates that thehuman KLK9 or mRNA can be utilized to diagnose of dermatologicaldiseases. Additionally the activity of the human KLK9 can be modulatedto treat those diseases.

Cancer Disorders

Cancer disorders within the scope of this definition comprise anydisease of an organ or tissue in mammals characterized by poorlycontrolled or uncontrolled multiplication of normal or abnormal cells inthat tissue and its effect on the body as a whole. Cancer diseaseswithin the scope of the definition comprise benign neoplasms,dysplasias, hyperplasias as well as neoplasms showing metastatic growthor any other transformations like e.g. leukoplakias which often precedea breakout of cancer. Cells and tissues are cancerous when they growmore rapidly than normal cells, displacing or spreading into thesurrounding healthy tissue or any other tissues of the body described asmetastatic growth, assume abnormal shapes and sizes, show changes intheir nucleocytoplasmatic ratio, nuclear polychromasia, and finally maycease. Cancerous cells and tissues may affect the body as a whole whencausing paraneoplastic syndromes or if cancer occurs within a vitalorgan or tissue, normal function will be impaired or halted, withpossible fatal results. The ultimate involvement of a vital organ bycancer, either primary or metastatic, may lead to the death of themammal affected. Cancer tends to spread, and the extent of its spread isusually related to an individual's chances of surviving the disease.Cancers are generally said to be in one of three stages of growth:early, or localized, when a tumor is still confined to the tissue oforigin, or primary site; direct extension, where cancer cells from thetumour have invaded adjacent tissue or have spread only to regionallymph nodes; or metastasis, in which cancer cells have migrated todistant parts of the body from the primary site, via the blood or lymphsystems, and have established secondary sites of infection. Cancer issaid to be malignant because of its tendency to cause death if nottreated. Benign tumors usually do not cause death, although they may ifthey interfere with a normal body function by virtue of their location,size, or paraneoplastic side effects. Hence benign tumors fall under thedefinition of cancer within the scope of this definition as well. Ingeneral, cancer cells divide at a higher rate than do normal cells, butthe distinction between the growth of cancerous and normal tissues isnot so much the rapidity of cell division in the former as it is thepartial or complete loss of growth restraint in cancer cells and theirfailure to differentiate into a useful, limited tissue of the type thatcharacterizes the functional equilibrium of growth of normal tissue.Cancer tissues may express certain molecular receptors and probably areinfluenced by the host's susceptibility and immunity and it is knownthat certain cancers of the breast and prostate, for example, areconsidered dependent on specific hormones for their existence. The term“cancer” under the scope of the definition is not limited to simplebenign neoplasia but comprises any other benign and malign neoplasialike 1) Carcinoma, 2) Sarcoma, 3) Carcinosarcoma, 4) Cancers of theblood-forming tissues, 5) tumors of nerve tissues including the brain,6) cancer of slin cells. Cancer according to 1) occurs in epithelialtissues, which cover the outer body (the skin) and line mucous membranesand the inner cavitary structures of organs e.g. such as the breast,lung, the respiratory and gastrointestinal tracts, the endocrine glands,and the genitourinary system. Ductal or glandular elements may persistin epithelial tumors, as in adenocarcinomas like e.g. thyroidadenocarcinoma, gastric adenocarcinoma, uterine adenocarcinoma. Cancersof the pavement-cell epithelium of the skin and of certain mucousmembranes, such as e.g. cancers of the tongue, lip, larynx, urinarybladder, uterine cervix, or penis, may be termed epidermoid orsquamous-cell carcinomas of the respective tissues and are in the scopeof the definition of cancer as well. Cancer according to 2) develops inconnective tissues, including fibrous tissues, adipose (fat) tissues,muscle, blood vessels, bone, and cartilage like e.g. osteogenic sarcoma;liposarcoma, fibrosarcoma, synovial sarcoma. Cancer according to 3) iscancer that develops in both epithelial and connective tissue. Cancerdisease within the scope of this definition may be primary or secondary,whereby primary indicates that the cancer originated in the tissue whereit is found rather than was established as a secondary site throughmetastasis from another lesion. Cancers and tumor diseases within thescope of this definition may be benign or malign and may affect allanatomical structures of the body of a mammal. By example but notlimited to they comprise cancers and tumor diseases of I) the bonemarrow and bone marrow derived cells (leukemias), II) the endocrine andexocrine glands like e.g. thyroid, parathyroid, pituitary, adrenalglands, salivary glands, pancreas III) the breast, like e.g. benign ormalignant tumors in the mammary glands of either a male or a female, themammary ducts, adenocarcinoma, medullary carcinoma, comedo carcinoma,Paget's disease of the nipple, inflammatory carcinoma of the youngwoman, IV) the lung, V) the stomach, VI) the liver and spleen, VII) thesmall intestine, VIII) the colon, IX) the bone and its supportive andconnective tissues like malignant or benign bone tumour, e.g. malignantosteogenic sarcoma, benign osteoma, cartilage tumors; like malignantchondrosarcoma or benign chondroma; bone marrow tumors like malignantmyeloma or benign eosinophilic granuloma, as well as metastatic tumorsfrom bone tissues at other locations of the body; X) the mouth, throat,larynx, and the esophagus, XI) the urinary bladder and the internal andexternal organs and structures of the urogenital system of male andfemale like ovaries, uterus, cervix of the uterus, testes, and prostategland, XII) the prostate, XIII) the pancreas, like ductal carcinoma ofthe pancreas; XIV) the lymphatic tissue like lymphomas and other tumorsof lymphoid origin, XV) the skin, XVI) cancers and tumor diseases of allanatomical structures belonging to the respiration and respiratorysystems including thoracal muscles and linings, XVI) primary orsecondary cancer of the lymph nodes XVIII) the tongue and of the bonystructures of the hard palate or sinuses, XVIV) the mouth, cheeks, neckand salivary glands, XX) the blood vessels including the heart and theirlinings, XXI) the smooth or skeletal muscles and their ligaments andlinings, XXII the peripheral, the autonomous, the central nervous systemincluding the cerebellum, XXIII) the adipose tissue.

The human KLK9 is highly expressed in the following cancer tissues:esophagus tumor, stomach tumor, colon tumor, ileum tumor, ovary tumor,breast tumor. The expression in the above mentioned tissues and inparticular the differential expression between diseased tissue esophagustumor and healthy tissue esophagus, between diseased tissue stomachtumor and healthy tissue stomach, between diseased tissue colon tumorand healthy tissue colon, between diseased tissue ileum tumor andhealthy tissue ileum, between diseased tissue ovary tumor and healthytissue, between diseased tissue breast tumor and healthy tissue breastdemonstrates that the human KLK9 or mRNA can be utilized to diagnose ofcancer. Additionally the activity of the human KLK9 can be modulated totreat cancer.

Inflammatory Diseases

Inflammatory diseases comprise diseases triggered by cellular ornon-cellular mediators of the immune system or tissues causing theinflammation of body tissues and subsequently producing an acute orchronic inflammatory condition. Examples for such inflammatory diseasesare hypersensitivity reactions of type I-IV, for example but not limitedto hypersensitivity diseases of the lung including asthma, atopicdiseases, allergic rhinitis or conjunctivitis, angioedema of the lids,hereditary angioedema, antireceptor hypersensitivity reactions andautoimmune diseases, Hashimoto's thyroiditis, systemic lupuserythematosus, Goodpasture's syndrome, pemphigus, myasthenia gravis,Grave's and Raynaud's disease, type B insulin-resistant diabetes,rheumatoid arthritis, psoriasis, Crohn's disease, scleroderma, mixedconnective tissue disease, polymyositis, sarcoidosis,glomerulonephritis, acute or chronic host versus graft reactions.

The human KLK9 is highly expressed in the following tissues of theimmune system and tissues responsive to components of the immune systemas well as in the following tissues responsive to mediators ofinflammation: ileum chronic inflammation, liver liver cirrhosis. Theexpression in the above mentioned tissues and in particular thedifferential expression between diseased tissue ileum chronicinflammation and healthy tissue ileum, between diseased tissue liverliver cirrhosis and healthy tissue liver demonstrates that the humanKLK9 or mRNA can be utilized to diagnose of inflammatory diseases.Additionally the activity of the human KLK9 can be modulated to treatinflammatory diseases.

Disorders Related to Urology

Genitourinary disorders comprise benign and malign disorders of theorgans constituting the genitourinary system of female and male, renaldiseases like acute or chronic renal failure, immunologically mediatedrenal diseases like renal transplant rejection, lupus nephritis, immunecomplex renal diseases, glomerulopathies, nephritis, toxic nephropathy,obstructive uropathies like benign prostatic hyperplasia (BPH),neurogenic bladder syndrome, urinary incontinence like urge-, stress-,or overflow incontinence, pelvic pain, and erectile dysfunction.

The human KLK9 is highly expressed in the following urological tissues:penis and corpus cavernosum. The expression in the above mentionedtissues demonstrates that the human KLK9 or mRNA can be utilized todiagnose of urological disorders. Additionally the activity of the humanKLK9 can be modulated to treat urological disorders.

Metabolic Disorders

Metabolic diseases are defined as conditions which result from anabnormality in any of the chemical or biochemical transformations andtheir regulating systems essential to producing energy, to regeneratingcellular constituents, to eliminating unneeded products arising fromthese processes, and to regulate and maintain homeostasis in a mammalregardless of whether acquired or the result of a genetictransformation. Depending on which metabolic pathway is involved, asingle defective transformation or disturbance of its regulation mayproduce consequences that are narrow, involving a single body function,or broad, affecting many organs, organ-systems or the body as a whole.Diseases resulting from abnormalities related to the fine and coarsemechanisms that affect each individual transformation, its rate anddirection or the availability of substrates like amino acids, fattyacids, carbohydrates, minerals, cofactors, hormones, regardless whetherthey are inborn or acquired, are well within the scope of the definitionof a metabolic disease according to this application.

Metabolic diseases often are caused by single defects in particularbiochemical pathways, defects that are due to the deficient activity ofindividual enzymes or molecular receptors leading to the regulation ofsuch enzymes. Hence in a broader sense disturbances of the underlyinggenes, their products and their regulation lie well within the scope ofthis definition of a metabolic disease. For example, but not limited to,metabolic diseases may affect 1) biochemical processes and tissuesubiquitous all over the body, 2) the bone, 3) the nervous system, 4) theendocrine system, 5) the muscle including the heart, 6) the skin andnervous tissue, 7) the urogenital system, 8) the homeostasis of bodysystems like water and electrolytes. For example, but not limited to,metabolic diseases according to 1) comprise obesity, amyloidosis,disturbances of the amino acid metabolism like branched chain disease,hyperaminoacidemia, hyperaminoaciduria, disturbances of the metabolismof urea, hyperammonemia, mucopolysaccharidoses e.g. Maroteaux-Lamysyndrom, storage diseases like glycogen storage diseases and lipidstorage diseases, glycogenosis diseases like Cori's disease,malabsorption diseases like intestinal carbohydrate malabsorption,oligosaccharidase deficiency like maltase-, lactase-,sucrase-insufficiency, disorders of the metabolism of fructose,disorders of the metabolism of galactose, galactosaemia, disturbances ofcarbohydrate utilization like diabetes, hypoglycemia, disturbances ofpyruvate metabolism, hypolipidemia, hypolipoproteinemia, hyperlipidemia,hyperlipoproteinemia, carnitine or carnitine acyltransferase deficiency,disturbances of the porphyrin metabolism, porphyrias, disturbances ofthe purine metabolism, lysosomal diseases, metabolic diseases of nervesand nervous systems like gangliosidoses, sphingolipidoses, sulfatidoses,leucodystrophies, Lesch-Nyhan syndrome. For example, but not limited to,metabolic diseases according to 2) comprise osteoporosis, osteomalacialike osteoporosis, osteopenia, osteogenesis imperfecta, osteopetrosis,osteonecrosis, Paget's disease of bone, hypophosphatemia. For example,but not limited to, metabolic diseases according to 3) comprisecerebellar dysfunction, disturbances of brain metabolism like dementia,Alzheimer's disease, Huntington's chorea, Parkinson's disease, Pick'sdisease, toxic encephalopathy, demyelinating neuropathies likeinflammatory neuropathy, Guillain-Barre syndrome. For example, but notlimited to, metabolic diseases according to 4) comprise primary andsecondary metabolic disorders associated with hormonal defects like anydisorder stemming from either an hyperfunction or hypoflnction of somehormone-secreting endocrine gland and any combination thereof. Theycomprise Sipple's syndrome, pituitary gland dysfunction and its effectson other endocrine glands, such as the thyroid, adrenals, ovaries, andtestes, acromegaly, hyper- and hypothyroidism, euthyroid goiter,euthyroid sick syndrome, thyroiditis, and thyroid cancer, over- orunderproduction of the adrenal steroid hormones, adrenogenital syndrome,Cushing's syndrome, Addison's disease of the adrenal cortex, Addison'spernicious anemia, primary and secondary aldosteronism, diabetesinsipidus, carcinoid syndrome, disturbances caused by the dysfunction ofthe parathyroid glands, pancreatic islet cell dysfunction, diabetes,disturbances of the endocrine system of the female like estrogendeficiency, resistant ovary syndrome. For example, but not limited to,metabolic diseases according to 5) comprise muscle weakness, myotonia,Duchenne's and other muscular dystrophies, dystrophia myotonica ofSteinert, mitochondrial myopathies like disturbances of the catabolicmetabolism in the muscle, carbohydrate and lipid storage myopathies,glycogenoses, myoglobinuria, malignant hyperthermia, polymyalgiarheumatica, dermatomyositis, primary myocardial disease, cardiomyopathy.For example, but not limited to, metabolic diseases according to 6)comprise disorders of the ectoderm, neurofibromatosis, scleroderma andpolyarteritis, Louis-Bar syndrome, von Hippel-Lindau disease,Sturge-Weber syndrome, tuberous sclerosis, amyloidosis, porphyria. Forexample, but not limited to, metabolic diseases according to 7) comprisesexual dysfunction of the male and female. For example, but not limitedto, metabolic diseases according to 8) comprise confused states andseizures due to inappropriate secretion of antidiuretic hormone from thepituitary gland, Liddle's syndrome, Bartter's syndrome, Fanconi'ssyndrome, renal electrolyte wasting, diabetes insipidus.

The human KLK9 is highly expressed in the following metabolic diseaserelated tissues: liver liver cirrhosis and adipose. The expression inthe above mentioned tissues and in particular the differentialexpression between diseased tissue liver liver cirrhosis and healthytissue liver demonstrates that the human KLK9 or mRNA can be utilized todiagnose of metabolic diseases. Additionally the activity of the humanKLK9 can be modulated to treat metabolic diseases.

Applications

The present invention provides for both prophylactic and therapeuticmethods for hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases.

The regulatory method of the invention involves contacting a cell withan agent that modulates one or more of the activities of KLK9. An agentthat modulates activity can be an agent as described herein, such as anucleic acid or a protein, a naturally-occurring cognate ligand of thepolypeptide, a peptide, a peptidomimetic, or any small molecule. In oneembodiment, the agent stimulates one or more of the biologicalactivities of KLK9. Examples of such stimulatory agents include theactive KLK9 and nucleic acid molecules encoding a portion of KLK9. Inanother embodiment, the agent inhibits one or more of the biologicalactivities of KLK9. Examples of such inhibitory agents include antisensenucleic acid molecules and antibodies. These regulatory methods can beperformed in vitro (e.g., by culturing the cell with the agent) or,alternatively, in vivo (e.g, by administering the agent to a subject).As such, the present invention provides methods of treating anindividual afflicted with a disease or disorder characterized byunwanted expression or activity of KLK9 or a protein in the KLK9signaling pathway. In one embodiment, the method involves administeringan agent like any agent identified or being identifiable by a screeningassay as described herein, or combination of such agents that modulatesay upregulate or downregulate the expression or activity of KLK9 or ofany protein in the KLK9 signaling pathway. In another embodiment, themethod involves administering a regulator of KLK9 as therapy tocompensate for reduced or undesirably low expression or activity of KLK9or a protein in the KLK9 signaling pathway.

Stimulation of activity or expression of KLK9 is desirable in situationsin which enzymatic activity or expression is abnormally low and in whichincreased activity is likely to have a beneficial effect. Conversely,inhibition of enzymatic activity or expression of KLK9 is desirable insituations in which activity or expression of KLK9 is abnormally highand in which decreasing its activity is likely to have a beneficialeffect.

This invention is further illustrated by the following examples whichshould not be construed as limiting. The contents of all references,patents and published patent applications cited throughout thisapplication are hereby incorporated by reference.

Pharmaceutical Compositions

This invention further pertains to novel agents identified by theabove-described screening assays and uses thereof for treatments asdescribed herein.

The nucleic acid molecules, polypeptides, and antibodies (also referredto herein as “active compounds”) of the invention can be incorporatedinto pharmaceutical compositions suitable for administration. Suchcompositions typically comprise the nucleic acid molecule, protein, orantibody and a pharmaceutically acceptable carrier. As used herein thelanguage “pharmaceutically acceptable carrier” is intended to includeany and all solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and thelike, compatible with pharmaceutical administration The use of suchmedia and agents for pharma-ceutically active substances is well knownin the art. Except insofar as any conventional media or agent isincompatible with the active compound, use thereof in the compositionsis contemplated. Supplementary active compounds can also be incorporatedinto the compositions.

The invention includes pharmaceutical compositions comprising aregulator of KLK9 expression or activity (and/or a regulator of theactivity or expression of a protein in the KLK9 signaling pathway) aswell as methods for preparing such compositions by combining one or moresuch regulators and a pharmaceutically acceptable carrier. Also withinthe invention are pharmaceutical compositions comprising a regulatoridentified using the screening assays of the invention packaged withinstructions for use. For regulators that are antagonists of KLK9activity or which reduce KLK9 expression, the instructions would specifyuse of the pharmaceutical composition for treatment of hematologicaldiseases, cardiovascular diseases, neurological diseases, metabolicdiseases, urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases. For regulatorsthat are agonists of KLK9 activity or increase KLK9 expression, theinstructions would specify use of the pharmaceutical composition fortreatment of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases.

An inhibitor of KLK9 may be produced using methods which are generallyknown in the art. In particular, purified KLK9 may be used to produceantibodies or to screen libraries of pharmaceutical agents to identifythose which specifically bind KLK9. Antibodies to KLK9 may also begenerated using methods that are well known in the art. Such antibodiesmay include, but are not limited to, polyclonal, monoclonal, chimeric,single chain antibodies, Fab fragments, and fragments produced by a Fabexpression library. Neutralizing antibodies like those which inhibitdimer formation are especially preferred for therapeutic use.

In another embodiment of the invention, the polynucleotides encodingKLK9, or any fragment or complement thereof, may be used for therapeuticpurposes. In one aspect, the complement of the polynucleotide encodingKLK9 may be used in situations in which it would be desirable to blockthe transcription of the mRNA. In particular, cells may be transformedwith sequences complementary to polynucleotides encoding KLK9. Thus,complementary molecules or fragments may be used to modulate KLK9activity, or to achieve regulation of gene function. Such technology isnow well known in the art, and sense or antisense oligonucleotides orlarger fragments can be designed from various locations along the codingor control regions of sequences encoding KLK9.

Expression vectors derived from retroviruses, adenoviruses, or herpes orvaccinia viruses, or from various bacterial plasmids, may be used fordelivery of nucleotide sequences to the targeted organ, tissue, or cellpopulation. Methods which are well known to those skilled in the art canbe used to construct vectors which will express nucleic acid sequencecomplementary to the polynucleotides of the gene encoding KLK9. Thesetechniques are described, for example, in [Scott and Smith (1990)].

Any of the therapeutic methods described above may be applied to anysubject in need of such therapy, including, for example, mammals such asdogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.

An additional embodiment of the invention relates to the administrationof a pharma-ceutical composition containing KLK9 in conjunction with apharmaceutically acceptable carrier, for any of the therapeutic effectsdiscussed above. Such pharma-ceutical compositions may consist of KLK9,antibodies to KLK9, and mimetics, agonists, antagonists, or inhibitorsof KLK9. The compositions may be administered alone or in combinationwith at least one other agent, such as a stabilizing compound, which maybe administered in any sterile, biocompatible pharmaceutical carrierincluding, but not limited to, saline, buffered saline, dextrose, andwater. The com-positions may be administered to a patient alone, or incombination with other agents, drugs or hormones.

A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. Examples of routesof administration include parenteral, e.g., intravenous, intradermal,subcutaneous, oral (e.g., inhalation), transdermal (topical),transmucosal, and rectal administration. Solutions or suspen-sions usedfor parenteral, intradermal, or subcutaneous application can include thefollowing components: a sterile diluent such as water for injection,saline solution, fixed oils, polyethylene glycols, glycerine, propyleneglycol or other synthetic solvents; antibacterial agents such as benzylalcohol or methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediaminetetraacetic acid;buffers such as acetates, citrates or phosphates and agents for theadjustment of tonicity such as sodium chloride or dextrose. pH can beadjusted with acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampoules,disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersions. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEM™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringability exists. It must be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, a pharmaceutically acceptable polyol like glycerol,propylene glycol, liquid polyetheylene glycol, and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousantibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in thecomposition. Prolonged absorption of the injectable compositions can bebrought about by including in the composition an agent which delaysabsorption, for example, aluminum monostearate and gelatin. Sterileinjectable solutions can be prepared by incorporating the activecompound (e.g., a polypeptide or antibody) in the required amount in anappropriate solvent with one or a combination of ingredients enumeratedabove, as required, followed by filtered sterilization.

Generally, dispersions are prepared by incorporating the active compoundinto a sterile vehicle which contains a basic dispersion medium and therequired other ingredients from those enumerated above. In the case ofsterile powders for the preparation of sterile injectable solutions, thepreferred methods of preparation are vacuum drying and freeze-dryingwhich yields a powder of the active ingredient plus any additionaldesired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an ediblecarrier. They can be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Oral compositions can also be preparedusing a fluid carrier for use as a mouthwash, wherein the compound inthe fluid carrier is applied orally and swished and expectorated orswallowed.

Pharmaceutically compatible binding agents, and/or adjuvant materialscan be included as part of the composition. The tablets, pills,capsules, troches and the like can contain any of the followingingredients, or compounds of a similar nature: a binder such asmicrocrystalline cellulose, gum tragacanth or gelatin; an excipient suchas starch or lactose, a disintegrating agent such as alginic acid,Primogel, or corn starch; a lubricant such as magnesium stearate orsterotes; a glidant such as colloidal silicon dioxide; a sweeteningagent such as sucrose or saccharin; or a flavoring agent such aspeppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in theform of an aerosol spray from a pressurized container or dispenser whichcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art, and include, forexample, for transmucosal administration, detergents, bile salts, andfusidic acid derivatives. Transmucosal administration can beaccomplished through the use of nasal sprays or suppositories. Fortransdermal administration, the active compounds are formulated intoointments, salves, gels, or creams as generally known in the art.

The compounds can also be prepared in the form of suppositories (e.g.,with conventional suppository bases such as cocoa butter and otherglycerides) or retention enemas for rectal delivery.

In one embodiment, the active compounds are prepared with carriers thatwill protect the compound against rapid elimination from the body, suchas a controlled release formulation, including implants andmicroencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions(including liposomes targeted to infected cells with monoclonalantibodies to viral antigens) can also be used as pharmaceuticallyacceptable carriers. These can be prepared according to methods known tothose skilled in the art, for example, as described in U.S. Pat. No.4,522,811.

It is especially advantageous to formulate oral or parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subject tobe treated; each unit containing a predetermined quantity of activecompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on the unique characteristics of the active compound and theparticular therapeutic effect to be achieved, and the limitationsinherent in the art of compounding such an active compound for thetreatment of individuals.

The pharmaceutical compositions can be included in a container, pack, ordispenser together with instructions for administration. Forpharmaceutical compositions which include an antagonist of KLK9activity, a compound which reduces expression of KLK9, or a compoundwhich reduces expression or activity of a protein in the KLK9 signalingpathway or any combination thereof, the instructions for administrationwill specify use of the composition for hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases. Forpharmaceutical compositions which include an agonist of KLK9 activity, acompound which increases expression of KLK9, or a compound whichincreases expression or activity of a protein in the KLK9 signalingpathway or any combination thereof, the instructions for administrationwill specify use of the composition for hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases.

Diagnostics

In another embodiment, antibodies which specifically bind KLK9 may beused for the diagnosis of disorders characterized by the expression ofKLK9, or in assays to monitor patients being treated with KLK9 oragonists, antagonists, and inhibitors of KLK9. Antibodies useful fordiagnostic purposes may be prepared in the same manner as thosedescribed above for therapeutics. Diagnostic assays for KLK9 includemethods which utilize the antibody and a label to detect KLK9 in humanbody fluids or in extracts of cells or tissues. The antibodies may beused with or without modification, and may be labeled by covalent ornon-covalent joining with a reporter molecule. A wide variety ofreporter molecules, several of which are described above, are known inthe art and may be used.

A variety of protocols for measuring KLK9, including ELISAs, RIAs, andFACS, are known in the art and provide a basis for diagnosing altered orabnormal levels of KLK9 expression. Normal or standard values for KLK9expression are established by combining body fluids or cell extractstaken from normal mammalian subjects, preferably human, with antibody toKLK9 under conditions suitable for complex formation. The amount ofstandard complex formation may be quantified by various methods,preferably by photometric means. Quantities of KLK9 expressed in subjectsamples from biopsied tissues are compared with the standard values.Deviation between standard and subject values establishes the parametersfor diagnosing disease.

In another embodiment of the invention, the polynucleotides encodingKLK9 may be used for diagnostic purposes. The polynucleotides which maybe used include oligo-nucleotide sequences, complementary RNA and DNAmolecules, and PNAs. The polynucleotides may be used to detect andquantitate gene expression in biopsied tissues in which expression ofKLK9 may be correlated with disease. The diagnostic assay may be used todistinguish between absence, presence, and excess expression of KLK9,and to monitor regulation of KLK9 levels during therapeuticintervention.

Polynucleotide sequences encoding KLK9 may be used for the diagnosis ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseasesassociated with expression of KLK9. The polynucleotide sequencesencoding KLK9 may be used in Southern, Northern, or dot-blot analysis,or other membrane-based technologies; in PCR technologies; in dipstick,pin, and ELISA assays; and in microarrays utilizing fluids or tissuesfrom patient biopsies to detect altered KLK9 expression. Suchqualitative or quantitative methods are well known in the art.

In a particular aspect, the nucleotide sequences encoding KLK9 may beuseful in assays that detect the presence of associated disorders,particularly those mentioned above. The nucleotide sequences encodingKLK9 may be labelled by standard methods and added to a fluid or tissuesample from a patient under conditions suitable for the formation ofhybridization complexes. After a suitable incubation period, the sampleis washed and the signal is quantitated and compared with a standardvalue. If the amount of signal in the patient sample is significantlyaltered from that of a comparable control sample, the nucleotidesequences have hybridized with nucleotide sequences in the sample, andthe presence of altered levels of nucleotide sequences encoding KLK9 inthe sample indicates the presence of the associated disorder. Suchassays may also be used to evaluate the efficacy of a particulartherapeutic treatment regimen in animal studies, in clinical trials, orin monitoring the treatment of an individual patient.

In order to provide a basis for the diagnosis of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases associated withexpression of KLK9, a normal or standard profile for expression isestablished. This may be accomplished by combining body fluids or cellextracts taken from normal subjects, either animal or human, with asequence, or a fragment thereof, encoding KLK9, under conditionssuitable for hybridization or amplification. Standard hybridization maybe quantified by comparing the values obtained from normal subjects withvalues from an experiment in which a known amount of a substantiallypurified polynucleotide is used. Standard values obtained from normalsamples may be compared with values obtained from samples from patientswho are symptomatic for a disorder. Deviation from standard values isused to establish the presence of a disorder.

Determination of a Therapeutically Effective Dose

The determination of a therapeutically effective dose is well within thecapability of those skilled in the art. A therapeutically effective doserefers to that amount of active ingredient which increases or decreasesKLK9 activity relative to KLK9 activity which occurs in the absence ofthe therapeutically effective dose. For any compound, thetherapeutically effective dose can be estimated initially either in cellculture assays or in animal models, usually mice, rabbits, dogs, orpigs. The animal model also can be used to determine the appropriateconcentration range and route of administration. Such information canthen be used to determine useful doses and routes for administration inhumans.

Therapeutic efficacy and toxicity, e.g., ED₅₀ (the dose therapeuticallyeffective in 50% of the population) and LD₅₀ (the dose lethal to 50% ofthe population), can be determined by standard pharmaceutical proceduresin cell cultures or experimental animals. The dose ratio of toxic totherapeutic effects is the therapeutic index, and it can be expressed asthe ratio, LD₅₀/ED₅₀. Pharmaceutical compositions which exhibit largetherapeutic indices are preferred. The data obtained from cell cultureassays and animal studies is used in formulating a range of dosage forhuman use. The dosage contained in such compositions is preferablywithin a range of circulating concentrations that include the ED₅₀ withlittle or no toxicity. The dosage varies within this range dependingupon the dosage form employed, sensitivity of the patient, and the routeof administration. The exact dosage will be determined by thepractitioner, in light of factors related to the subject that requirestreatment. Dosage and administration are adjusted to provide sufficientlevels of the active ingredient or to maintain the desired effect.Factors which can be taken into account include the severity of thedisease state, general health of the subject, age, weight, and gender ofthe subject, diet, time and frequency of administration, drugcombination(s), reaction sensitivities, and tolerance/response totherapy. Long-acting pharmaceutical compositions can be administeredevery 3 to 4 days, every week, or once every two weeks depending on thehalf-life and clearance rate of the particular formulation.

Normal dosage amounts can vary from 0.1 micrograms to 100,000micrograms, up to a total dose of about 1 g, depending upon the route ofadministration. Guidance as to particular dosages and methods ofdelivery is provided in the literature and generally available topractitioners in the art. Those skilled in the art will employ differentformulations for nucleotides than for proteins or their inhibitors.Similarly, delivery of polynucleotides or polypeptides will be specificto particular cells, conditions, locations, etc. If the reagent is asingle-chain antibody, polynucleotides encoding the antibody can beconstructed and introduced into a cell either ex vivo or in vivo usingwell-established techniques including, but not limited to,transferrin-polycation-mediated DNA transfer, transfection with naked orencapsulated nucleic acids, liposome-mediated cellular fusion,intracellular transportation of DNA-coated latex beads, protoplastfusion, viral infection, electroporation, “gene gun”, and DEAE- orcalcium phosphate-mediated transfection.

If the expression product is mRNA, the reagent is preferably anantisense oligo-nucleotide or a ribozyme. Polynucleotides which expressantisense oligonucleotides or ribozymes can be introduced into cells bya variety of methods, as described above. Preferably, a reagent reducesexpression of KLK9 gene or the activity of KLK9 by at least about 10,preferably about 50, more preferably about 75, 90, or 100% relative tothe absence of the reagent. The effectiveness of the mechanism chosen todecrease the level of expression of KLK9 gene or the activity of KLK9can be assessed using methods well known in the art, such ashybridization of nucleotide probes to KLK9-specific mRNA, quantitativeRT-PCR, immunologic detection of KLK9, or measurement of KLK9 activity.

In any of the embodiments described above, any of the pharmaceuticalcompositions of the invention can be administered in combination withother appropriate therapeutic agents. Selection of the appropriateagents for use in combination therapy can be made by one of ordinaryskill in the art, according to conventional pharmaceutical principles.The combination of therapeutic agents can act synergistically to effectthe treatment or prevention of the various disorders described above.Using this approach, one may be able to achieve therapeutic efficacywith lower dosages of each agent, thus reducing the potential foradverse side effects. Any of the therapeutic methods described above canbe applied to any subject in need of such therapy, including, forexample, mammals such as dogs, cats, cows, horses, rabbits, monkeys, andmost preferably, humans.

Nucleic acid molecules of the invention are those nucleic acid moleculeswhich are contained in a group of nucleic acid molecules consisting of(i) nucleic acid molecules encoding a polypeptide comprising the aminoacid sequence of SEQ ID NO: 2, (ii) nucleic acid molecules comprisingthe sequence of SEQ ID NO: 1, (iii) nucleic acid molecules having thesequence of SEQ ID NO: 1, (iv)nucleic acid molecules the complementarystrand of which hybridizes under stringent conditions to a nucleic acidmolecule of (i), (ii), or (iii); and (v) nucleic acid molecules thesequence of which differs from the sequence of a nucleic acid moleculeof (iii) due to the degeneracy of the genetic code, wherein thepolypeptide encoded by said nucleic acid molecule has KLK9 activity.

Polypeptides of the invention are those polypeptides which are containedin a group of polypeptides consisting of (i) polypeptides having thesequence of SEQ ID NO: 2, (ii) polypeptides comprising the sequence ofSEQ ID NO: 2, (iii) polypeptides encoded by nucleic acid molecules ofthe invention and (iv) polypeptides which show at least 99%, 98%, 95%,90%, or 80% homology with a polypeptide of (i), (ii), or (iii), whereinsaid purified polypeptide has KLK9 activity.

An object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising the steps of (i)contacting a test compound with a KLK9 polypeptide, (ii) detect bindingof said test compound to said KLK9 polypeptide. E.g., compounds thatbind to the KLK9 polypeptide are identified potential therapeutic agentsfor such a disease.

Another object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising the steps of (i)determining the activity of a KLK9 polypeptide at a certainconcentration of a test compound or in the absence of said testcompound, (ii) determining the activity of said polypeptide at adifferent concentration of said test compound. E.g., compounds that leadto a difference in the activity of the KLK9 polypeptide in (i) and (ii)are identified potential therapeutic agents for such a disease.

Another object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising the steps of (i)determining the activity of a KLK9 polypeptide at a certainconcentration of a test compound, (ii) determining the activity of aKLK9 polypeptide at the presence of a compound known to be a regulatorof a KLK9 polypeptide. E.g., compounds that show similar effects on theactivity of the KLK9 polypeptide in (i) as compared to compounds used in(ii) are identified potential therapeutic agents for such a disease.

Other objects of the invention are methods of the above, wherein thestep of contacting is in or at the surface of a cell.

Other objects of the invention are methods of the above, wherein thecell is in vitro.

Other objects of the invention are methods of the above, wherein thestep of contacting is in a cell-free system.

Other objects of the invention are methods of the above, wherein thepolypeptide is coupled to a detectable label.

Other objects of the invention are methods of the above, wherein thecompound is coupled to a detectable label.

Other objects of the invention are methods of the above, wherein thetest compound displaces a ligand which is first bound to thepolypeptide.

Other objects of the invention are methods of the above, wherein thepolypeptide is attached to a solid support.

Other objects of the invention are methods of the above, wherein thecompound is attached to a solid support.

Another object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising the steps of (i)contacting a test compound with a KLK9 polynucleotide, (ii) detectbinding of said test compound to said KLK9 polynucleotide. Compoundsthat, e.g., bind to the KLK9 polynucleotide are potential therapeuticagents for the treatment of such diseases.

Another object of the invention is the method of the above, wherein thenucleic acid molecule is RNA.

Another object of the invention is a method of the above, wherein thecontacting step is in or at the surface of a cell.

Another object of the invention is a method of the above, wherein thecontacting step is in a cell-free system.

Another object of the invention is a method of the above, wherein thepolynucleotide is coupled to a detectable label.

Another object of the invention is a method of the above, wherein thetest compound is coupled to a detectable label.

Another object of the invention is a method of diagnosing a diseasecomprised in a group of diseases consisting of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammalcomprising the steps of (i) determining the amount of a KLK9polynucleotide in a sample taken from said mammal, (ii) determining theamount of KLK9 polynucleotide in healthy and/or diseased mammal. Adisease is diagnosed, e.g., if there is a substantial similarity in theamount of KLK9 polynucleotide in said test mammal as compared to adiseased mammal.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising a therapeutic agent which binds to a KLK9 polypeptide.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising a therapeutic agent which regulates the activity of aKLK9 polypeptide.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising a therapeutic agent which regulates the activity of aKLK9 polypeptide, wherein said therapeutic agent is (i) a smallmolecule, (ii) an RNA molecule, (iii) an antisense oligonucleotide, (iv)a polypeptide, (v) an antibody, or (vi) a ribozyme.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising a KLK9 polynucleotide.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising a KLK9 polypeptide.

Another object of the invention is the use of regulators of a KLK9 forthe preparation of a pharmaceutical composition for the treatment of adisease comprised in a group of diseases consisting of hematologicaldiseases, cardiovascular diseases, neurological diseases, metabolicdiseases, urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammal.

Another object of the invention is a method for the preparation of apharmaceutical composition useful for the treatment of a diseasecomprised in a group of diseases consisting of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammalcomprising the steps of (i) identifying a regulator of KLK9, (ii)determining whether said regulator ameliorates the symptoms of a diseasecomprised in a group of diseases consisting of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammal;and (iii) combining of said regulator with an acceptable pharmaceuticalcarrier.

Another object of the invention is the use of a regulator of KLK9 forthe regulation of KLK9 activity in a mammal having a disease comprisedin a group of diseases consisting of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases.

The examples below are provided to illustrate the subject invention.These examples are provided by way of illustration and are not includedfor the purpose of limiting the invention.

EXAMPLES Example 1 Search for Homologous Sequences in Public SequenceData Bases

The degree of homology can readily be calculated by known methods.Preferred methods to determine homology are designed to give the largestmatch between the sequences tested. Methods to determine homology arecodified in publicly available computer programs such as BestFit,BLASTP, BLASTN, and FASTA. The BLAST programs are publicly availablefrom NCBI and other sources in the internet.

For KLK9 the following hits to known sequences were identified by usingthe BLAST algorithm [Altschul S F, Madden T L, Schaffer A A, Zhang J,Zhang Z, Miller W, Lipman D J; Nucleic Acids Res 1997 September 1;25(17): 3389-402] and the following set of parameters: matrix=BLOSUM62and low complexity filter. The following databases were searched: NCBI(non-redundant database) and DERWENT patent database (Geneseq).

The following hits were found: >gi|29366811|ref|NM_012315.1| Homosapiens kallikrein 9 (KLK9), mRNA Length = 1438 Score = 1493 bits (753),Expect = 0.0 Identities = 753/753 (100%) >gi|27485322|ref|XM_210377.1|Homo sapiens similar to Kallikrein 9 precursor (Kallikrein-like protein3) (KLK-L3) (LOC284366), mRNA Length = 753 Score = 1493 bits (753),Expect = 0.0 Identities = 753/ 753(100%) >gi|4589278|gb|AF135026.1|AF135026 Homo sapiens kallikrein-likeprotein 3 (KLK9) gene, complete cds, alternatively spliced Length = 8622Score = 527 bits (266), Expect = e−147 Identities = 266/266(100%) >gi|11244757|gb|AF243527.1|AF243527 Homo sapiens serine proteasegene cluster, complete sequence Length = 230000 Score = 527 bits (266),Expect = e−147 Identities = 266/266(100%) >gi|10799392|gb|AC011473.4|AC011473 Homo sapiens chromosome 19,BAC BC349142 (CTC-518B2), complete sequence Length = 132323 Score = 527bits (266), Expect = e−147 Identities = 266/266(100%) >gi|27731316|ref|XM_218647.1| Rattus norvegicus similar toKallikrein 9 precursor (Kallikrein-like protein 3) (KLK-L3) (LOC292851),mRNA Length = 759 Score = 208 bits (105), Expect = 9e−51 Identities =222/261 (85%) >gi|20827398|ref|XM_133405.1| Mus musculus expressedsequence AI324041 (AI324041), mRNA Length = 1116 Score = 182 bits (92),Expect = 5e−43 Identities = 191/224 (85%) >gi|12836265|dbj|AK004807.1|Mus musculus adult male lung cDNA, RIKEN full-length enriched library,clone: 1200016C12 product: similar to KALLIKREIN 9 PRECURSOR (EC3.4.21.—) (KALLIKREIN-LIKE PROTEIN 3) (KLK-L3) [Homo sapiens], fullinsert sequence Length = 1048 Score = 147 bits (74), Expect = 3e−32Identities = 247/305 (80%)

Example 2 Expression Profiling

Total cellular RNA was isolated from cells by one of two standardmethods: 1) guanidine isothiocyanate/Cesium chloride density gradientcentrifugation [Kellogg, (1990)]; or with the Tri-Reagent protocolaccording to the manufacturer's specifications (Molecular ResearchCenter, Inc., Cincinatti, Ohio). Total RNA prepared by the Tri-reagentprotocol was treated with DNAse I to remove genomic DNA contamination.

For relative quantitation of the mRNA distribution of KLK9, total RNAfrom each cell or tissue source was first reverse transcribed. 85 μg oftotal RNA was reverse transcribed using 1 μmole random hexamer primers,0.5 mM each of dATP, dCTP, dGTP and dTTP (Qiagen, Hilden, Germany), 3000U RnaseQut (Invitrogen, Groningen, Netherlands) in a final volume of 680μl. The first strand synthesis buffer and Omniscript reversetranscriptase (2 u/μl) were from (Qiagen, Hilden, Germany). The reactionwas incubated at 37° C. for 90 minutes and cooled on ice.

The volume was adjusted to 6800 μl with water, yielding a finalconcentration of 12.5 ng/μl of starting RNA.

For relative quantitation of the distribution of KLK9 mRNA in cells andtissues the PerkinElmer ABI Prism RTM. 7700 Sequence Detection system orBiorad iCycler was used according to the manufacturer's specificationsand protocols. PCR reactions were set up to quantitate KLK9 and thehousekeeping genes HPRT (hypoxanthine phosphoribosyltransferase), GAPDH(glyceraldehyde-3-phosphate dehydrogenase), β-actin, and others. Forwardand reverse primers and probes for KLK9 were designed using thePerkinElmer ABI Primer Express™ software and were synthesized byTibMolBiol (Berlin, Germany). The KLK9 forward primer sequence was:Primer1 (SEQ ID NO: 3). The KLK9 reverse primer sequence was Primer2(SEQ ID NO: 4). Probe1 (SEQ ID NO: 5), labelled with FAM(carboxyfluorescein succinimidyl ester) as the reporter dye and TAMRA(carboxytetramethylrhodamine) as the quencher, is used as a probe forKLK9. The following reagents were prepared in a total of 25 μl: 1×TaqManbuffer A, 5.5 mM MgCl₂, 200 nM of dATP, dCTP, dGTP, and dUTP, 0.025 U/μlAmpliTaq Gold™, 0.01 U/μl AmpErase and Probel (SEQ ID NO: 4), KLK9forward and reverse primers each at 200 nM, 200 nM KLK9FAM/TAMRA-labelled probe, and 5 μl of template cDNA. Thermal cyclingparameters were 2 min at 50° C., followed by 10 min at 95° C., followedby 40 cycles of melting at 95° C. for 15 sec and annealing/extending at60° C. for 1 min.

Calculation of corrected CT values

The CT (threshold cycle) value is calculated as described in the“Quantitative determination of nucleic acids” section. The CF-value(factor for threshold cycle correction) is calculated as follows:

-   1. PCR reactions were set up to quantitate the housekeeping genes    (HKG) for each cDNA sample.-   2. CT_(HKG)-values (threshold cycle for housekeeping gene) were    calculated as described in the “Quantitative determination of    nucleic acids” section.-   3. CT_(HKG)-mean values (CT mean value of all HKG tested on one    cDNAs) of all HKG for each cDNA are calculated (n=number of HKG):    CT_(HKG-n)-mean value=(CT_(HKG1)-value+CT_(HKG2)-value+ . . .    +CT_(HKG-n)-value)/n-   4. CT_(pannel) mean value (CT mean value of all HKG in all tested    cDNAs)=(CT_(HKG1)-mean value+CT_(HKG2)-mean value+ . . .    +CT_(HKG-y)-mean value)/y (y=number of cDNAs)-   5. CF_(cDNA-n) (correction factor for cDNA n)=CT_(pannel)-mean    value−CT_(HKG-n)-mean value-   6. CT_(cDNA-n) (CT value of the tested gene for the cDNA    n)+CF_(cDNA-n) (correction factor for cDNA n)=CT_(cor-cDNA-n)    (corrected CT value for a gene on cDNA n)    Calculation of Relative Expression    Definition: highest CT_(cor-cDNA-n)≠40 is defined as CT_(cor-cDNA)    [high] Relative Expression=2^((CTcor-cDNA[high]CTcor-cDNA-n))    Tissues

The expression of KLK9 was investigated in the tissues in table 1.

Expression Profile

The results of the the mRNA-quantification (expression profiling) isshown in Table 1. TABLE 1 Relative expression of KLK9 in various humantissues. fetal heart 6 heart 1 pericardium 33 heart atrium (right) 12heart atrium (left) 263 heart ventricle (left) 843 interventricularseptum 13 fetal aorta 11 aorta 1323 artery 704 coronary artery 2 vein498 coronary artery smooth muscle primary cells 119 HUVEC cells 96 skin949 adrenal gland 0 thyroid 2 thyroid tumor 9 pancreas 0 pancreas livercirrhosis 16 esophagus 2180 esophagus tumor 99 stomach 1 stomach tumor329 colon 0 colon tumor 215 small intestine 18 ileum 288 ileum tumor 75ileum chronic inflammation 1380 rectum 508 salivary gland 0 fetal liver2 liver 10 liver liver cirrhosis 739 liver tumor 100 HEP G2 cells 62leukocytes (peripheral blood) 20 Jurkat (T-cells) 49 bone marrow 0erythrocytes 119 lymphnode 617 thymus 1 thrombocytes 714 bone marrowCD71+ cells 55 bone marrow CD34+ cells 115 bone marrow CD15+ cells 399cord blood CD71+ cells 139 spleen 16 spleen liver cirrhosis 3 skeletalmuscle 78 adipose 191 fetal brain 3 brain 11 Alzheimer brain 229cerebellum 30 cerebellum (right) 187 cerebellum (left) 739 cerebralcortex 229 Alzheimer cerebral cortex 74 frontal lobe 214 Alzheimer brainfrontal lobe 478 occipital lobe 461 parietal lobe 51 temporal lobe 30precentral gyrus 27 postcentral gyrus 458 tonsilla cerebelli 198 vermiscerebelli 154 pons 101 substantia nigra 315 cerebral meninges 1121cerebral peduncles 73 corpus callosum 201 hippocampus 244 thalamus 62dorsal root ganglia 923 spinal cord 62 neuroblastoma SK-N-MC cells 164neuroblastoma SH-SY5Y cells 136 neuroblastoma IMR32 cells 360 retina2288 fetal lung 8 fetal lung fibroblast IMR-90 cells 3 lung 0 lung tumor556 lung COPD 133 trachea 4 cervix 22 testis 82 HeLa cells (cervixtumor) 0 placenta 0 uterus 75 uterus tumor 27 ovary tumor 465 breast 739breast tumor 153 MDA MB 231 cells (breast tumor) 48 mammary gland 31prostate 17 prostate BPH 30 bladder 0 penis 592 corpus cavernosum 179fetal kidney 34 kidney 8 kidney tumor 64 HEK 293 cells 113

Example 3 Antisense Analysis

Knowledge of the correct, complete cDNA sequence coding for KLK9 enablesits use as a tool for antisense technology in the investigation of genefunction. Oligonucleotides, cDNA or genomic fragments comprising theantisense strand of a polynucleotide coding for KLK9 are used either invitro or in vivo to inhibit translation of the mRNA. Such technology isnow well known in the art, and antisense molecules can be designed atvarious locations along the nucleotide sequences. By treatment of cellsor whole test animals with such antisense sequences, the gene ofinterest is effectively turned off. Frequently, the function of the geneis ascertained by observing behavior at the intracellular, cellular,tissue or organismal level (e.g., lethality, loss of differentiatedfunction, changes in morphology, etc.).

In addition to using sequences constructed to interrupt transcription ofa particular open reading frame, modifications of gene expression isobtained by designing antisense sequences to intron regions,promoter/enhancer elements, or even to trans-acting regulatory genes.

Example 4 Expression of KLK9

Expression of KLK9 is accomplished by subcloning the cDNAs intoappropriate expression vectors and transfecting the vectors intoexpression hosts such as, e.g., E. coli. In a particular case, thevector is engineered such that it contains a promoter forβ-galactosidase, upstream of the cloning site, followed by sequencecontaining the amino-terminal Methionine and the subsequent sevenresidues of β-galactosidase. Immediately following these eight residuesis an engineered bacteriophage promoter useful for artificial primingand transcription and for providing a number of unique endonucleaserestriction sites for cloning.

Induction of the isolated, transfected bacterial strain withIsopropyl-β-D-thio-galactopyranoside (IPTG) using standard methodsproduces a fusion protein corresponding to the first seven residues ofβ-galactosidase, about 15 residues of “linker”, and the peptide encodedwithin the cDNA. Since cDNA clone inserts are generated by anessentially random process, there is probability of 33% that theincluded cDNA will lie in the correct reading frame for propertranslation. If the cDNA is not in the proper reading frame, it isobtained by deletion or insertion of the appropriate number of basesusing well known methods including in vitro mutagenesis, digestion withexonuclease III or mung bean nuclease, or the inclusion of anoligonucleotide linker of appropriate length.

The KLK9 cDNA is shuttled into other vectors known to be useful forexpression of proteins in specific hosts. Oligonucleotide primerscontaining cloning sites as well as a segment of DNA (about 25 bases)sufficient to hybridize to stretches at both ends of the target cDNA issynthesized chemically by standard methods. These primers are then usedto amplify the desired gene segment by PCR. The resulting gene segmentis digested with appropriate restriction enzymes under standardconditions and isolated by gel electrophoresis. Alternately, similargene segments are produced by digestion of the cDNA with appropriaterestriction enzymes. Using appropriate primers, segments of codingsequence from more than one gene are ligated together and cloned inappropriate vectors. It is possible to optimize expression byconstruction of such chimeric sequences.

Suitable expression hosts for such chimeric molecules include, but arenot limited to, mammalian cells such as Chinese Hamster Ovary (CHO) andhuman 293 cells., insect cells such as Sf9 cells, yeast cells such asSaccharomyces cerevisiae and bacterial cells such as E. coli. For eachof these cell systems, a useful expression vector also includes anorigin of replication to allow propagation in bacteria, and a selectablemarker such as the β-lactamase antibiotic resistance gene to allowplasmid selection in bacteria. In addition, the vector may include asecond selectable marker such as the neomycin phosphotransferase gene toallow selection in transfected eukaryotic host cells. Vectors for use ineukaryotic expression hosts require RNA processing elements such as ₃′polyadenylation sequences if such are not part of the cDNA of interest.

Additionally, the vector contains promoters or enhancers which increasegene expression. Such promoters are host specific and include MMTV,SV40, and metallothionine promoters for CHO cells; trp, lac, tac and T7promoters for bacterial hosts; and alpha factor, alcohol oxidase and PGHpromoters for yeast. Transcription enhancers, such as the rous sarcomavirus enhancer, are used in mammalian host cells. Once homogeneouscultures of recombinant cells are obtained through standard culturemethods, large quantities of recombinantly produced KLK9 are recoveredfrom the conditioned medium and analyzed using chromatographic methodsknown in the art. For example, KLK9 can be cloned into the expressionvector pcDNA3, as exemplified herein. This product can be used totransform, for S example, HEK293 or COS by methodology standard in theart. Specifically, for example, using Lipofectamine (Gibco BRL catologno. 18324-020) mediated gene transfer.

Example 5 Isolation of Recombinant KLK9

KLK9 is expressed as a chimeric protein with one or more additionalpolypeptide domains added to facilitate protein purification. Suchpurification facilitating domains include, but are not limited to, metalchelating peptides such as histidine-tryptophan modules that allowpurification on immobilized metals [Appa Rao, 1997] and the domainutilized in the FLAGS extension/affinity purification system (ImmunexCorp., Seattle, Wash.). The inclusion of a cleavable linker sequencesuch as Factor Xa or enterokinase (Invitrogen, Groningen, TheNetherlands) between the purification domain and the KLK9 sequence isuseful to facilitate expression of KLK9.

The following example provides a method for purifying KLK9.

KLK9 is generated using the baculovirus expression system BAC-TO-BAC(GIBCO BRL) based on Autographa californica nuclear polyhedrosis virus(AcNPV) infection of Spodoptera frugiperda insect cells (Sf9 cells).

cDNA encoding proteases cloned into either the donor plasmid pFASTBAC1or pFASTBAC-HT which contain a mini-Tn7 transposition element. Therecombinant plasmid is transformed into DH10BAC competent cells whichcontain the parent bacmid bMON14272 (AcNPV infectious DNA) and a helperplasmid. The mini-Tn7 element on the pFASTBAC donor can transpose to theattTn7 attachment site on the bacmid thus introducing the protease geneinto the viral genome. Colonies containing recombinant bacmids areidentified by disruption of the lacZ gene. The protease/bacmid constructcan then be isolated and infected into insect cells (Sf9 cells)resulting in the production of infectious recombinant baculovirusparticles and expression of either unfused recombinant enzyme(pFastbac1) or KLK9-His fusion protein (pFastbacHT).

Cells are harvested and extracts prepared 24, 48 and 72 hours aftertransfection. Expression of KLK9 is confirmed by coomassie stainingafter sodium dodecyl sulphate-polyacrylamide gel electrophoresis(SDS-PAGE) and western blotting onto a PVDF membrane of an unstainedSDS-PAGE. The protease-His fusion protein is detected due to theinteraction between the Ni-NTA HRP conjugate and the His-tag which isfused to KLK9.

Example 6 Production of KLK9 Specific Antibodies

Two approaches are utilized to raise antibodies to KLK9, and eachapproach is useful for generating either polyclonal or monoclonalantibodies. In one approach, denatured protein from reverse phase HPLCseparation is obtained in quantities up to 75 mg. This denatured proteinis used to immunize mice or rabbits using standard protocols; about 100μg are adequate for immunization of a mouse, while up to 1 mg might beused to immunize a rabbit. For identifying mouse hybridomas, thedenatured protein is radioiodinated and used to screen potential murineB-cell hybridomas for those which produce antibody. This procedurerequires only small quantities of protein, such that 20 mg is sufficientfor labeling and screening of several thousand clones.

In the second approach, the amino acid sequence of an appropriate KLK9domain, as deduced from translation of the cDNA, is analyzed todetermine regions of high antigenicity. Oligopeptides comprisingappropriate hydrophilic regions are synthesized and used in suitableimmunization protocols to raise antibodies. The optimal amino acidsequences for immunization are usually at the C-terminus, the N-terminusand those intervening, hydrophilic regions of the polypeptide which arelikely to be exposed to the external environment when the protein is inits natural conformation.

Typically, selected peptides, about 15 residues in length, aresynthesized using an Applied Biosystems Peptide Synthesizer Model 431Ausing fmoc-chemistry and coupled to keyhole limpet hemocyanin (KLH;Sigina, St. Louis, Mo.) by reaction withM-maleimidobenzoyl-N-hydroxysuccinimide ester, MBS. If necessary, acysteine is introduced at the N-terminus of the peptide to permitcoupling to KLH. Rabbits are immunized with the peptide-KLH complex incomplete Freund's adjuvant. The resulting antisera are tested forantipeptide activity by binding the peptide to plastic, blocking with 1%bovine serum albumin, reacting with antisera, washing and reacting withlabeled (radioactive or fluorescent), affinity purified, specific goatanti-rabbit IgG.

Hybridomas are prepared and screened using standard techniques.Hybridomas of interest are detected by screening with labeled KLK9 toidentify those fusions producing the monoclonal antibody with thedesired specificity. In a typical protocol, wells of plates (FAST;Becton-Dickinson, Palo Alto, Calif.) are coated during incubation withaffinity purified, specific rabbit anti-mouse (or suitable antispecies 1g) antibodies at 10 mg/ml. The coated wells are blocked with 1% bovineserum albumin, (BSA), washed and incubated with supernatants fromhybridomas. After washing the wells are incubated with labeled KLK9 at 1mg/ml. Supernatants with specific antibodies bind more labeled KLK9 thanis detectable in the background. Then clones producing specificantibodies are expanded and subjected to two cycles of cloning atlimiting dilution. Cloned hybridomas are injected into pristane-treatedmice to produce ascites, and monoclonal antibody is purified from mouseascitic fluid by affinity chromatography on Protein A. Monoclonalantibodies with affinities of at least 10⁸ M⁻¹, preferably 10⁹ to 10¹⁰M⁻¹ or stronger, are typically made by standard procedures.

Example 7 Diagnostic Test Using KLK9 Specific Antibodies

Particular KLK9 antibodies are useful for investigating signaltransduction and the diagnosis of infectious or hereditary conditionswhich are characterized by differences in the amount or distribution ofKLK9 or downstream products of an active signaling cascade.

Diagnostic tests for KLK9 include methods utilizing antibody and a labelto detect KLK9 in human body fluids, membranes, cells, tissues orextracts of such. The polypeptides and antibodies of the presentinvention are used with or without modification. Frequently, thepolypeptides and antibodies are labeled by joining them, eithercovalently or noncovalently, with a substance which provides for adetectable signal. A wide variety of labels and conjugation techniquesare known and have been reported extensively in both the scientific andpatent literature. Suitable labels include radionuclides, enzymes,substrates, cofactors, inhibitors, fluorescent agents, chemiluminescentagents, chromogenic agents, magnetic particles and the like.

A variety of protocols for measuring soluble or membrane-bound KLK9,using either polyclonal or monoclonal antibodies specific for theprotein, are known in the art. Examples include enzyme-linkedimmunosorbent assay (ELISA), radioimmunoassay (RIA) and fluorescentactivated cell sorting (FACS). A two-site monoclonal-based immunoassayutilizing monoclonal antibodies reactive to two non-interfering epitopeson KLK9 is preferred, but a competitive binding assay may be employed.

Example 8 Purification of Native KLK9 Using Specific Antibodies

Native or recombinant KLK9 is purified by immunoaffinity chromatographyusing antibodies specific for KLK9. In general, an immunoaffinity columnis constructed by covalently coupling the anti-TRH antibody to anactivated chromatographic resin.

Polyclonal immmunoglobulins are prepared from immune sera either byprecipitation with ammonium sulfate or by purification on immobilizedProtein A (Pharmacia LKB Biotechnology, Piscataway N.J.). Likewise,monoclonal antibodies are prepared from mouse ascites fluid by ammoniumsulfate precipitation or chromatography on immobilized Protein A.Partially purified immunoglobulin is covalently attached to achromatographic resin such as CnBr-activated Sepharose (Phannacia LKBBiotechnology). The antibody is coupled to the resin, the resin isblocked, and the derivative resin is washed according to themanufacturer's instructions.

Such immunoaffinity columns are utilized in the purification of KLK9 bypreparing a fraction from cells containing KLK9 in a soluble form. Thispreparation is derived by solubilization of whole cells or of asubcellular fraction obtained via differential centrifugation (with orwithout addition of detergent) or by other methods well known in theart. Alternatively, soluble KLK9 containing a signal sequence issecreted in useful quantity into the medium in which the cells aregrown.

A soluble KLK9-containing preparation is passed over the immunoaffinitycolumn, and the column is washed under conditions that allow thepreferential absorbance of KLK9 (e.g., high ionic strength buffers inthe presence of detergent). Then, the column is eluted under conditionsthat disrupt antibody/protein binding (e.g., a buffer of pH 2-3 or ahigh concentration of a chaotrope such as urea or thiocyanate ion), andKLK9 is collected.

Example 9 Drug Screening

This invention is particularly useful for screening therapeuticcompounds by using KLK9 or fragments thereof in any of a variety of drugscreening techniques. The following example provides a system for drugscreening measuring the protease activity.

The recombinant protease-His fusion protein can be purified from thecrude lysate by metal-affinity chromatography using Ni-NTA agarose. Thisallows the specific retention of the recombinant material (since this isfused to the His-tag) whilst the endogenous insect proteins are washedoff. The recombinant material is then eluted by competition withimidazol.

The activity of KLK9 molecules of the present invention can be measuredusing a variety of assays that measure KLK9 activity. For example, KLK9enzyme activity can be assessed by a standard in vitro serine/metallo/ .. . protease assay (see, for example, [U.S. Pat. No. 5,057,414]). Thoseof skill in the art are aware of a variety of substrates suitable for invitro assays, such as SucAla-Ala-Pro-Phe-pNA, fluoresceinmono-p-guanidinobenzoate hydrochloride,benzyloxycarbonyl-L-Arginyl-S-benzylester, Nalpha-Benzoyl-L-arginineethyl ester hydrochloride, and the like. In addition, protease assaykits available from commercial sources, such as Calbiochem™ (San Diego,Calif.). For general references, see Barrett (Ed.), Methods inEnzymology, Proteolytic Enzymes: Serine and Cysteine Peptidases(Academic Press Inc. 1994), and Barrett et al., (Eds.), Handbook ofProteolytic Enzymes (Academic Press Inc. 1998).

Example 10 Rational Drug Design

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides of interest or of small molecules withwhich they interact, agonists, antagonists, or inhibitors. Any of theseexamples are used to fashion drugs which are more active or stable formsof the polypeptide or which enhance or interfere with the function of apolypeptide in vivo.

In one approach, the three-dimensional structure of a protein ofinterest, or of a protein-inhibitor complex, is determined by x-raycrystallography, by computer modeling or, most typically, by acombination of the two approaches. Both the shape and charges of thepolypeptide must be ascertained to elucidate the structure and todetermine active site(s) of the molecule. Less often, useful informationregarding the structure of a polypeptide is gained by modeling based onthe structure of homologous proteins. In both cases, relevant structuralinformation is used to design efficient inhibitors. Useful examples ofrational drug design include molecules which have improved activity orstability or which act as inhibitors, agonists, or antagonists of nativepeptides.

It is also possible to isolate a target-specific antibody, selected byfunctional assay, as described above, and then to solve its crystalstructure. This approach, in principle, yields a pharmacore upon whichsubsequent drug design is based. It is possible to bypass proteincrystallography altogether by generating anti-idiotypic antibodies(anti-ids) to a functional, pharmacologically active antibody. As amirror image of a mirror image, the binding site of the anti-ids isexpected to be an analog of the original receptor. The anti-id is thenused to identify and isolate peptides from banks of chemically orbiologically produced peptides. The isolated peptides then act as thepharmacore.

By virtue of the present invention, sufficient amount of polypeptide aremade available to perform such analytical studies as X-raycrystallography. In addition, knowledge of the KLK9 amino acid sequenceprovided herein provides guidance to those employing computer modelingtechniques in place of or in addition to x-ray crystallography.

Example 11 Identification of Other Members of the Signal TransductionComplex

Labeled KLK9 is useful as a reagent for the purification of moleculeswith which it interacts. In one embodiment of affinity purification,KLK9 is covalently coupled to a chromatography column. Cell-free extractderived from synovial cells or putative target cells is passed over thecolumn, and molecules with appropriate affinity bind to KLK9.KLK9-complex is recovered from the column, and the KLK9-binding liganddisassociated and subjected to N-terminal protein sequencing. The aminoacid sequence information is then used to identify the captured moleculeor to design degenerate oligonucleotide probes for cloning the relevantgene from an appropriate cDNA library.

In an alternate method, antibodies are raised against KLK9, specificallymonoclonal antibodies. The monoclonal antibodies are screened toidentify those which inhibit the binding of labeled KLK9. Thesemonoclonal antibodies are then used thera-peutically.

Example 12 Use and Administration of Antibodies, Inhibitors, orAntagonists

Antibodies, inhibitors, or antagonists of KLK9 or other treatments andcompunds that are limiters of signal transduction (LSTs), providedifferent effects when administered therapeutically. LSTs are formulatedin a nontoxic, inert, pharmaceutically acceptable aqueous carrier mediumpreferably at a pH of about 5 to 8, more preferably 6 to 8, although pHmay vary according to the characteristics of the antibody, inhibitor, orantagonist being formulated and the condition to be treated.Characteristics of LSTs include solubility of the molecule, itshalf-life and antigenicity/immunogenicity. These and othercharacteristics aid in defining an effective carrier. Native humanproteins are preferred as LSTs, but organic or synthetic moleculesresulting from drug screens are equally effective in particularsituations.

LSTs are delivered by known routes of administration including but notlimited to topical creams and gels; transmucosal spray and aerosol;transdermal patch and bandage; injectable, intravenous and lavageformulations; and orally administered liquids and pills particularlyformulated to resist stomach acid and enzymes. The particularformulation, exact dosage, and route of administration is determined bythe attending physician and varies according to each specific situation.

Such determinations are made by considering multiple variables such asthe condition to be treated, the LST to be administered, and thepharmacokinetic profile of a particular LST. Additional factors whichare taken into account include severity of the disease state, patient'sage, weight, gender and diet, time and frequency of LST administration,possible combination with other drugs, reaction sensitivities, andtolerance/response to therapy. Long acting LST formulations might beadministered every 3 to 4 days, every week, or once every two weeksdepending on half-life and clearance rate of the particular LST.

Normal dosage amounts vary from 0.1 to 10⁵ μg, up to a total dose ofabout 1 g, depending upon the route of administration. Guidance as toparticular dosages and methods of delivery is provided in theliterature; see U.S. Pat. Nos. 4,657,760; 5,206,344; or 5,225,212. Thoseskilled in the art employ different formulations for different LSTs.Administration to cells such as nerve cells necessitates delivery in amanner different from that to other cells such as vascular endothelialcells.

It is contemplated that abnormal signal transduction, trauma, ordiseases which trigger KLK9 activity are treatable with LSTs. Theseconditions or diseases are specifically diagnosed by the tests discussedabove, and such testing should be performed in suspected cases of viral,bacterial or fungal infections, allergic responses, mechanical injuryassociated with trauma, hereditary diseases, lymphoma or carcinoma, orother conditions which activate the genes of lymphoid or neuronaltissues.

Example 13 Production of Non-human Transgenic Animals

Animal model systems which elucidate the physiological and behavioralroles of the KLK9 are produced by creating nonhuman transgenic animalsin which the activity of the KLK9 is either increased or decreased, orthe amino acid sequence of the expressed KLK9 is altered, by a varietyof techniques. Examples of these techniques include, but are not limitedto: 1) Insertion of normal or mutant versions of DNA encoding a KLK9, bymicroinjection, electroporation, retroviral transfection or other meanswell known to those skilled in the art, into appropriately fertilizedembryos in order to produce a transgenic animal or 2) homologousrecombination of mutant or normal, human or animal versions of thesegenes with the native gene locus in transgenic animals to alter theregulation of expression or the structure of these KLK9 sequences. Thetechnique of homologous recombination is well known in the art. Itreplaces the native gene with the inserted gene and hence is useful forproducing an animal that cannot express native KLK9s but does express,for example, an inserted mutant KLK9, which has replaced the native KLK9in the animal's genome by recombination, resulting in underexpression ofthe transporter. Microinjection adds genes to the genome, but does notremove them, and the technique is useful for producing an animal whichexpresses its own and added KLK9, resulting in overexpression of theKLK9.

One means available for producing a transgenic animal, with a mouse asan example, is as follows: Female mice are mated, and the resultingfertilized eggs are dissected out of their oviducts. The eggs are storedin an appropriate medium such as cesiumchloride M2 medium. DNA or cDNAencoding KLK9 is purified from a vector by methods well known to the oneskilled in the art. Inducible promoters may be fused with the codingregion of the DNA to provide an experimental means to regulateexpression of the transgene. Alternatively or in addition, tissuespecific regulatory elements may be fused with the coding region topermit tissue-specific expression of the transgene. The DNA, in anappropriately buffered solution, is put into a microinjection needle(which may be made from capillary tubing using a piper puller) and theegg to be injected is put in a depression slide. The needle is insertedinto the pronucleus of the egg, and the DNA solution is injected. Theinjected egg is then transferred into the oviduct of a pseudopregnantmouse which is a mouse stimulated by the appropriate hormones in orderto maintain false pregnancy, where it proceeds to the uterus, implants,and develops to term. As noted above, microinjection is not the onlymethod for inserting DNA into the egg but is used here only forexemplary purposes.

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1. A method of screening for therapeutic agents useful in the treatmentof a disease selected from the group consisting of hematologicaldiseases, cardiovascular diseases, neurological diseases, metabolicdiseases, urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammalcomprising the steps of i) contacting a test compound with a KLK9polypeptide, and ii) detecting binding of said test compound to saidKLK9 polypeptide.
 2. A method of screening for therapeutic agents usefulin the treatment of a disease selected from the group consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising the steps of i) determining the activity of a KLK9polypeptide at a certain concentration of a test compound or in theabsence of said test compound, and ii) determining the activity of saidpolypeptide at a different concentration of said test compound.
 3. Amethod of screening for therapeutic agents useful in the treatment of aselected from the group consisting of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammalcomprising the steps of i) determining the activity of a KLK9polypeptide at a certain concentration of a test compound, and ii)determining the activity of a KLK9 polypeptide at the presence of acompound known to be a regulator of a KLK9 polypeptide.
 4. The method ofclaim 1, wherein the step of contacting is in or at the surface of acell.
 5. The method of claim 1, wherein the cell is in vitro.
 6. Themethod of claim 1, wherein the step of contacting is in a cell-freesystem.
 7. The method of claim 1, wherein the polypeptide is coupled toa detectable label.
 8. The method of claim 1, wherein the compound iscoupled to a detectable label.
 9. The method of claim 1, wherein thetest compound displaces a ligand which is first bound to thepolypeptide.
 10. The method of claim 1, wherein the polypeptide isattached to a solid support.
 11. The method of claim 1, wherein thecompound is attached to a solid support.
 12. A method of screening fortherapeutic agents useful in the treatment of a disease selected fromthe group consisting of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising the steps of i)contacting a test compound with a KLK9 polynucleotide, and ii) detectingbinding of said test compound to said KLK9 polynucleotide.
 13. Themethod of claim 12 wherein the nucleic acid molecule is RNA.
 14. Themethod of claim 12 wherein the contacting step is in or at the surfaceof a cell.
 15. The method of claim 12 wherein the contacting step is ina cell-free system.
 16. The method of claim 12 wherein polynucleotide iscoupled to a detectable label.
 17. The method of claim 12 wherein thetest compound is coupled to a detectable label.
 18. A method ofdiagnosing a disease selected from the group consisting of hematologicaldiseases, cardiovascular diseases, neurological diseases, metabolicdiseases, urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammalcomprising the steps of i) determining the amount of a KLK9polynucleotide in a sample taken from said mammal, and ii) determiningthe amount of KLK9 polynucleotide in healthy and/or diseased mammals.19-20. (canceled)
 21. A pharmaceutical composition for the treatment ofa disease selected from the group consisting of hematological diseases,cardiovascular diseases, neurological diseases, metabolic diseases,urological diseases, cancer disorders, inflammation disorders,dermatological diseases and gastroenterological diseases in a mammalcomprising a therapeutic agent which regulates the activity of a KLK9polypeptide, wherein said therapeutic agent is i) a small molecule, ii)an RNA molecule, iii) an antisense oligonucleotide, iv) a polypeptide,v) an antibody, or vi) a ribozyme.
 22. A pharmaceutical composition forthe treatment of a disease selected from the group consisting ofhematological diseases, cardiovascular diseases, neurological diseases,metabolic diseases, urological diseases, cancer disorders, inflammationdisorders, dermatological diseases and gastroenterological diseases in amammal comprising a KLK9 polynucleotide.
 23. A pharmaceuticalcomposition for the treatment of a disease selected from the groupconsisting of hematological diseases, cardiovascular diseases,neurological diseases, metabolic diseases, urological diseases, cancerdisorders, inflammation disorders, dermatological diseases andgastroenterological diseases in a mammal comprising a KLK9 polypeptide.24-26. (canceled)